Deprecate cov_to_corr_matrix (#269)

* deprecate cov_to_corr_matrix * change import for deprecated * Update setup.py fix setup.py * Update requirements.txt add mne dependency to requirement file for doc only * Update Dockerfile remove protobuf install in Dockerfile (now by default in setup.py) * Update light_benchmark.py flake8 # noqa: E231 * Update plot_financial_data.py flake8 * Update light_benchmark.yml trigger benchmark on change to setup.py * [pre-commit.ci] auto fixes from pre-commit.com hooks * Update testing.yml as per actions/setup-python#850 (comment) --------- Co-authored-by: gcattan <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
pyRiemann · Apr 23, 2024 · 4ddf866 · 4ddf866
1 parent 6e4c49e
commit 4ddf866
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Showing 9 changed files with 23 additions and 9 deletions.
diff --git a/.github/workflows/light_benchmark.yml b/.github/workflows/light_benchmark.yml
@@ -7,6 +7,7 @@ on:
     - 'examples/**'
     - '.github/workflows/light_benchmark.yml'
     - 'benchmarks/light_benchmark.py'
+    - 'setup.py'
 
 jobs:
   light_benchmark:

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
@@ -18,6 +18,12 @@ jobs:
       matrix:
         python-version: [3.9, "3.10", 3.11]
         os: [ubuntu-latest, macOS-latest, windows-latest]
+        # Python 3.9 is on macos-13 but not macos-latest (macos-14-arm64)
+        # https://github.com/actions/setup-python/issues/696#issuecomment-1637587760
+        exclude:
+        - { python-version: "3.9", os: "macos-latest" }
+        include:
+        - { python-version: "3.9", os: "macos-13" }
 
     steps:
     - uses: actions/checkout@v4

diff --git a/Dockerfile b/Dockerfile
@@ -24,7 +24,6 @@ RUN mkdir /root/mne_data
 RUN mkdir /home/mne_data
 
 ## Workaround for firestore
-RUN pip install protobuf==4.25.3
 RUN pip install google_cloud_firestore==2.16.0
 ### Missing __init__ file in protobuf
 RUN touch /usr/local/lib/python3.9/site-packages/protobuf-4.25.3-py3.9.egg/google/__init__.py

diff --git a/benchmarks/light_benchmark.py b/benchmarks/light_benchmark.py
@@ -143,7 +143,7 @@
 
 
 def set_output(key: str, value: str):
-    print(f"::set-output name={key}::{value}")
+    print(f"::set-output name={key}::{value}")  # noqa: E231
 
 
 is_pr = sys.argv[1] == "pr"

diff --git a/doc/requirements.txt b/doc/requirements.txt
@@ -3,6 +3,7 @@ sphinx-gallery
 sphinx-bootstrap_theme
 numpydoc
 cython
+mne==1.6.1
 mne[data]>=0.24
 seaborn>=0.12.1
 scikit-learn==1.3.2

diff --git a/examples/other_datasets/plot_financial_data.py b/examples/other_datasets/plot_financial_data.py
@@ -395,13 +395,13 @@ def transform(self, X):
 print(
     f"Classical SVM: {train_score_svm:.3f}\
     \nQuantum SVM: {train_score_qsvm:.3f}\
-    \nClassical RandomForest: {train_score_rf:.3f}"
+    \nClassical RandomForest: {train_score_rf:.3f}"  # noqa: E231
 )
 print("----Testing score:----")
 print(
     f"Classical SVM: {score_svm:.3f}\
     \nQuantum SVM: {score_qsvm:.3f}\
-    \nClassical RandomForest: {score_rf:.3f}"
+    \nClassical RandomForest: {score_rf:.3f}"  # noqa: E231
 )
 
 

diff --git a/pyriemann_qiskit/utils/docplex.py b/pyriemann_qiskit/utils/docplex.py
@@ -13,7 +13,8 @@
 from qiskit_optimization.algorithms import CobylaOptimizer, MinimumEigenOptimizer
 from qiskit_optimization.converters import IntegerToBinary
 from qiskit_optimization.translators import from_docplex_mp
-from pyriemann_qiskit.utils import cov_to_corr_matrix, get_simulator
+from pyriemann.utils.covariance import normalize
+from pyriemann_qiskit.utils import get_simulator
 
 
 _global_optimizer = [None]
@@ -460,7 +461,7 @@ def __init__(self, upper_bound=7, quantum_instance=None):
     """
 
     def convert_covmat(self, covmat):
-        corr = cov_to_corr_matrix(covmat)
+        corr = normalize(covmat, "corr")
         return np.round(corr * self.upper_bound, 0)
 
     """Helper to create a docplex representation of a

diff --git a/pyriemann_qiskit/utils/math.py b/pyriemann_qiskit/utils/math.py
@@ -1,9 +1,13 @@
 """Module for mathematical helpers"""
-
-from pyriemann.utils.covariance import normalize
+from typing_extensions import deprecated
 import numpy as np
+from pyriemann.utils.covariance import normalize
 
 
+@deprecated(
+    "cov_to_corr_matrix is deprecated and will be removed in 0.4.0; "
+    "please use pyriemann.utils.covariance.normalize."
+)
 def cov_to_corr_matrix(covmat):
     """Convert covariance matrices to correlation matrices.
 

diff --git a/setup.py b/setup.py
@@ -45,6 +45,8 @@
                         'cvxpy==1.4.2',
                         'scipy==1.11.4',
                         'docplex==2.25.236',
+                        'grpcio-status==1.62.1',
+                        'protobuf==4.25.3',
                         'firebase_admin==6.4.0',
                         'scikit-learn==1.3.2',
                         'tqdm',
@@ -54,7 +56,7 @@
                                 'sphinx-gallery',
                                 'sphinx-bootstrap_theme',
                                 'numpydoc',
-                                'mne',
+                                'mne==1.6.1',
                                 'seaborn>=0.12.1',
                                 'moabb>=1.0.0',
                                 'imbalanced-learn==0.12.0'