Merge pull request #23 from smoia/enh/decorator

Better check functions input, transforming physio_or_numpy function into decorator

Author: smoia

.all-contributorsrc

@@ -10,6 +10,15 @@
   "commit": false,
   "commitConvention": "none",
   "contributors": [
+    {
+      "login": "mathdugre",
+      "name": "Mathieu Dugré",
+      "avatar_url": "https://avatars.githubusercontent.com/u/16450132?v=4",
+      "profile": "https://github.com/mathdugre",
+      "contributions": [
+        "code"
+      ]
+    },
     {
       "login": "goodalse2019",
       "name": "Sarah Goodale",
@@ -39,7 +48,9 @@
       "avatar_url": "https://avatars.githubusercontent.com/u/77584086?v=4",
       "profile": "https://github.com/me-pic",
       "contributions": [
-        "infra"
+        "infra",
+        "review",
+        "bug"
       ]
     },
     {

.github/workflows/auto-release.yml

@@ -1,6 +1,6 @@
-# # This workflows will create a release using auto when a PR is merged in master.
+# This workflows will create a release using auto when a PR is merged in master.
 
-name: Format and auto-release on PR merge
+name: Auto-release on PR merge
 
 on:
   # ATM, this is the closest trigger to a PR merging
@@ -10,7 +10,7 @@ on:
 
 jobs:
   auto-release:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     # Set skip ci to avoid loops
     if: "!contains(github.event.head_commit.message, 'ci skip') && !contains(github.event.head_commit.message, 'skip ci')"
     # Set bash as default shell for jobs
@@ -19,7 +19,7 @@ jobs:
         shell: bash
     steps:
     - name: Checkout source
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
       with:
         # Fetch all history for all branches and tags
         fetch-depth: 0

.github/workflows/python-publish.yml

@@ -1,5 +1,5 @@
-# # This workflows will upload a Python Package using Twine when a release is created
-# # For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
 
 name: Upload Python Package
 
@@ -10,15 +10,15 @@ on:
 jobs:
   deploy:
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     steps:
     - name: Checkout source
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.6'
+        python-version: 3.11
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
@@ -29,4 +29,5 @@ jobs:
         TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
       run: |
         python setup.py sdist bdist_wheel
+        twine check dist/*
         twine upload dist/*

.zenodo.json

@@ -23,6 +23,25 @@
           "type": "personal"
         }
       },
+      {
+        "affiliations": [
+          {
+            "name": "Concordia University"
+          }
+        ],
+        "person_or_org": {
+          "family_name": "Dugré",
+          "given_name": "Mathieu",
+          "identifiers": [
+            {
+              "identifier": "0000-0003-2828-6031",
+              "scheme": "orcid"
+            }
+          ],
+          "name": "Dugré, Mathieu",
+          "type": "personal"
+        }
+      },
       {
         "affiliations": [
           {

README.md

@@ -24,7 +24,7 @@ physioQC
 [![Supports python version](https://img.shields.io/pypi/pyversions/physioqc)](https://pypi.org/project/physioqc/)
 
 <!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
-[![All Contributors](https://img.shields.io/badge/all_contributors-7-orange.svg?style=flat-square)](#contributors-)
+[![All Contributors](https://img.shields.io/badge/all_contributors-8-orange.svg?style=flat-square)](#contributors-)
 <!-- ALL-CONTRIBUTORS-BADGE:END -->
 
 ``physioqc`` is a python3 library meant to do something.
@@ -70,12 +70,15 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
 <table>
   <tbody>
     <tr>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/mathdugre"><img src="https://avatars.githubusercontent.com/u/16450132?v=4?s=100" width="100px;" alt="Mathieu Dugré"/><br /><sub><b>Mathieu Dugré</b></sub></a><br /><a href="https://github.com/physiopy/physioqc/commits?author=mathdugre" title="Code">💻</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/goodalse2019"><img src="https://avatars.githubusercontent.com/u/60117796?v=4?s=100" width="100px;" alt="Sarah Goodale"/><br /><sub><b>Sarah Goodale</b></sub></a><br /><a href="#eventOrganizing-goodalse2019" title="Event Organizing">📋</a> <a href="#ideas-goodalse2019" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/physiopy/physioqc/pulls?q=is%3Apr+reviewed-by%3Agoodalse2019" title="Reviewed Pull Requests">👀</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/smoia"><img src="https://avatars.githubusercontent.com/u/35300580?v=4?s=100" width="100px;" alt="Stefano Moia"/><br /><sub><b>Stefano Moia</b></sub></a><br /><a href="https://github.com/physiopy/physioqc/commits?author=smoia" title="Code">💻</a> <a href="#ideas-smoia" title="Ideas, Planning, & Feedback">🤔</a> <a href="#infra-smoia" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="#projectManagement-smoia" title="Project Management">📆</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/me-pic"><img src="https://avatars.githubusercontent.com/u/77584086?v=4?s=100" width="100px;" alt="Marie-Eve Picard"/><br /><sub><b>Marie-Eve Picard</b></sub></a><br /><a href="#infra-me-pic" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/me-pic"><img src="https://avatars.githubusercontent.com/u/77584086?v=4?s=100" width="100px;" alt="Marie-Eve Picard"/><br /><sub><b>Marie-Eve Picard</b></sub></a><br /><a href="#infra-me-pic" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="https://github.com/physiopy/physioqc/pulls?q=is%3Apr+reviewed-by%3Ame-pic" title="Reviewed Pull Requests">👀</a> <a href="https://github.com/physiopy/physioqc/issues?q=author%3Ame-pic" title="Bug reports">🐛</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/celprov"><img src="https://avatars.githubusercontent.com/u/77437752?v=4?s=100" width="100px;" alt="celprov"/><br /><sub><b>celprov</b></sub></a><br /><a href="https://github.com/physiopy/physioqc/commits?author=celprov" title="Code">💻</a> <a href="#ideas-celprov" title="Ideas, Planning, & Feedback">🤔</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/SRSteinkamp"><img src="https://avatars.githubusercontent.com/u/17494653?v=4?s=100" width="100px;" alt="Simon Steinkamp"/><br /><sub><b>Simon Steinkamp</b></sub></a><br /><a href="https://github.com/physiopy/physioqc/commits?author=SRSteinkamp" title="Code">💻</a> <a href="#ideas-SRSteinkamp" title="Ideas, Planning, & Feedback">🤔</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/RayStick"><img src="https://avatars.githubusercontent.com/u/50215726?v=4?s=100" width="100px;" alt="Rachael Stickland"/><br /><sub><b>Rachael Stickland</b></sub></a><br /><a href="#infra-RayStick" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a></td>
+    </tr>
+    <tr>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/neuralkn0t"><img src="https://avatars.githubusercontent.com/u/86740625?v=4?s=100" width="100px;" alt="Neuralkn0t"/><br /><sub><b>Neuralkn0t</b></sub></a><br /><a href="https://github.com/physiopy/physioqc/commits?author=neuralkn0t" title="Code">💻</a></td>
     </tr>
   </tbody>

physioqc/metrics/multimodal.py

@@ -26,6 +26,7 @@ def signal_fct(signal):
     return signal
 
 
+@physio_or_numpy
 def std(signal):
     """
     Calculate standard deviation across input channels of signal.
@@ -40,11 +41,11 @@ def std(signal):
     N-sized array :obj:`numpy.ndarray`
         Standard deviation of signal.
     """
-    signal = physio_or_numpy(signal)
     std_val = np.std(signal, axis=0)
     return std_val
 
 
+@physio_or_numpy
 def mean(signal: np.array):
     """
     Calculate mean across input channels of signal.
@@ -59,11 +60,11 @@ def mean(signal: np.array):
     N-sized array :obj:`numpy.ndarray`
         Mean of signal.
     """
-    signal = physio_or_numpy(signal)
     mean_val = np.mean(signal, axis=0)
     return mean_val
 
 
+@physio_or_numpy
 def tSNR(signal):
     """
     Calculate temporal signal to noise ratio of signal.
@@ -78,11 +79,11 @@ def tSNR(signal):
     N-sized array :obj:`numpy.ndarray`
         Temporal signal to noise ratio of signal.
     """
-    signal = physio_or_numpy(signal)
     tSNR_val = np.mean(signal, axis=0) / np.std(signal, axis=0)
     return tSNR_val
 
 
+@physio_or_numpy
 def CoV(signal):
     """
     Calculate coefficient of variation of signal.
@@ -97,11 +98,11 @@ def CoV(signal):
     N-sized array :obj:`numpy.ndarray`
         Temporal signal to noise ratio of signal.
     """
-    signal = physio_or_numpy(signal)
     cov_val = np.std(signal, axis=0) / np.mean(signal, axis=0)
     return cov_val
 
 
+@physio_or_numpy
 def min(signal: np.array):
     """
     Calculate min across input channels of signal.
@@ -116,11 +117,11 @@ def min(signal: np.array):
     N-sized array :obj:`numpy.ndarray`
         min of signal.
     """
-    signal = physio_or_numpy(signal)
     min_val = np.min(signal, axis=0)
     return min_val
 
 
+@physio_or_numpy
 def max(signal: np.array):
     """
     Calculate max across input channels of signal.
@@ -135,11 +136,11 @@ def max(signal: np.array):
     N-sized array :obj:`numpy.ndarray`
         max of signal.
     """
-    signal = physio_or_numpy(signal)
     max_val = np.max(signal, axis=0)
     return max_val
 
 
+@physio_or_numpy
 def iqr(signal: np.array, q_high: float = 75, q_low: float = 25):
     """Calculate the Inter Quantile Range (IQR) over the input signal.
 
@@ -157,13 +158,13 @@ def iqr(signal: np.array, q_high: float = 75, q_low: float = 25):
     np.array
         iqr of the signal
     """
-    signal = physio_or_numpy(signal)
     p_high, p_low = np.percentile(signal, [q_high, q_low], axis=0)
     iqr_val = p_high - p_low
 
     return iqr_val
 
 
+@physio_or_numpy
 def percentile(signal: np.array, perc: float = 2):
     """Calculate the percentile perc over the signal.
 
@@ -179,7 +180,6 @@ def percentile(signal: np.array, perc: float = 2):
     np.array
         percentile of the signal
     """
-    signal = physio_or_numpy(signal)
     perc_val = np.percentile(signal, axis=0, q=perc)
 
     return perc_val

physioqc/metrics/utils.py

@@ -1,5 +1,6 @@
 """Miscellaneous utility functions for metric calculation."""
 
+import functools
 import logging
 
 LGR = logging.getLogger(__name__)
@@ -32,24 +33,29 @@ def print_metric_call(metric, args):
     LGR.info(msg)
 
 
-def physio_or_numpy(signal):
+def physio_or_numpy(func):
     """
-    Return data from a peakdet.physio.Physio object or a np.ndarray-like object.
+    Check if the function input is a Physio object or a np.ndarray-like object.
+
+    The "signal" argument must always be the first one.
 
     Parameters
     ----------
-    data : peakdet.physio.Physio, np.ndarray, or list
-        object to get data from
+    func: function to run the wrapper around
 
     Returns
     -------
-    np.ndarray-like object
-        Either a np.ndarray or a list
+    function
     """
-    if hasattr(signal, "history"):
-        signal = signal.data
 
-    return signal
+    @functools.wraps(func)
+    def wrapper(*args, **kwargs):
+        # signal must always be args[0]
+        if hasattr(args[0], "history"):
+            args[0] = args[0].data
+        return func(*args, **kwargs)
+
+    return wrapper
 
 
 def has_peakfind_physio(signal) -> bool:

setup.cfg

@@ -2,17 +2,14 @@
 name = physioqc
 url = https://github.com/physiopy/physioqc
 download_url = https://github.com/physiopy/physioqc
-author = Physiopy community
-maintainer = Stefano Moia
+author = The Physiopy Community
+maintainer = The Physiopy Community
 maintainer_email = [email protected]
 classifiers =
-    Development Status :: 1 - Planning
+    Development Status :: 3 - Alpha
     Intended Audience :: Science/Research
     License :: OSI Approved :: Apache Software License
-    Programming Language :: Python :: 3.7
-    Programming Language :: Python :: 3.8
-    Programming Language :: Python :: 3.9
-    Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3
 license = Apache-2.0
 description = A toolbox to run automatic quality control of physiological data.
 long_description = file:README.md