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#9 Update to 1.2.1 and backport patch for ppc64le/aarch64 test failures
Merged 2 years ago by music. Opened 2 years ago by music.
rpms/ music/python-mne v1.2.1  into  rawhide

file modified
+1 
@@ -15,3 +15,4 @@ 
 

  /python-mne-0.24.1.tar.gz
 

  /python-mne-1.0.3.tar.gz
 

  /python-mne-1.2.0.tar.gz
 

+ /python-mne-1.2.1.tar.gz

file added
+86 
@@ -0,0 +1,86 @@ 
 

+ From 24e7e3e0ebe41aa27f31b0d97c1d761479c19dad Mon Sep 17 00:00:00 2001
 

+ From: Eric Larson <larson.eric.d@gmail.com>
 

+ Date: Fri, 28 Oct 2022 11:53:49 -0400
 

+ Subject: [PATCH] BUG: Work around ppc64le bugs (#11284)
 

+ 

+ ---
 

+  azure-pipelines.yml                  | 2 +-
 

+  mne/inverse_sparse/mxne_optim.py     | 2 +-
 

+  mne/time_frequency/tests/test_tfr.py | 2 ++
 

+  mne/time_frequency/tfr.py            | 7 ++++++-
 

+  requirements.txt                     | 2 +-
 

+  5 files changed, 11 insertions(+), 4 deletions(-)
 

+ 

+ diff --git a/azure-pipelines.yml b/azure-pipelines.yml
 

+ index ee96d030a..08970b3dc 100644
 

+ --- a/azure-pipelines.yml
 

+ +++ b/azure-pipelines.yml
 

+ @@ -116,7 +116,7 @@ stages:
 

+      - bash: |
 

+          set -e
 

+          python -m pip install --progress-bar off --upgrade pip setuptools wheel codecov
 

+ -        python -m pip install --progress-bar off mne-qt-browser[opengl] pyvista scikit-learn pytest-error-for-skips python-picard "PySide6!=6.3.0,!=6.4.0" qtpy
 

+ +        python -m pip install --progress-bar off mne-qt-browser[opengl] pyvista scikit-learn pytest-error-for-skips python-picard "PySide6!=6.3.0,!=6.4.0,!=6.4.0.1" qtpy
 

+          python -m pip uninstall -yq mne
 

+          python -m pip install --progress-bar off --upgrade -e .[test]
 

+        displayName: 'Install dependencies with pip'
 

+ diff --git a/mne/inverse_sparse/mxne_optim.py b/mne/inverse_sparse/mxne_optim.py
 

+ index 8b7f342b5..587f17444 100644
 

+ --- a/mne/inverse_sparse/mxne_optim.py
 

+ +++ b/mne/inverse_sparse/mxne_optim.py
 

+ @@ -225,7 +225,7 @@ def _mixed_norm_solver_bcd(M, G, alpha, lipschitz_constant, maxit=200,
 

+                  # equivalent to:
 

+                  # z = np.linalg.solve(C, np.ones(K))
 

+                  u, s, _ = np.linalg.svd(C, hermitian=True)
 

+ -                if s[-1] <= 1e-6 * s[0]:
 

+ +                if s[-1] <= 1e-6 * s[0] or not np.isfinite(s).all():
 

+                      logger.debug("Iteration %d: LinAlg Error" % (i + 1))
 

+                      continue
 

+                  z = ((u * 1 / s) @ u.T).sum(0)
 

+ diff --git a/mne/time_frequency/tests/test_tfr.py b/mne/time_frequency/tests/test_tfr.py
 

+ index 57feb97ca..c626e9058 100644
 

+ --- a/mne/time_frequency/tests/test_tfr.py
 

+ +++ b/mne/time_frequency/tests/test_tfr.py
 

+ @@ -99,6 +99,8 @@ def test_time_frequency():
 

+          tfr_morlet(epochs_nopicks,
 

+                     freqs=freqs, n_cycles=n_cycles, use_fft=True,
 

+                     return_itc=False, picks=picks, average=False)
 

+ +    assert_allclose(
 

+ +        epochs_power_picks.data[0, 0, 0, 0], 9.130315e-23, rtol=1e-4)
 

+      power_picks_avg = epochs_power_picks.average()
 

+      # the actual data arrays here are equivalent, too...
 

+      assert_allclose(power.data, power_picks.data)
 

+ diff --git a/mne/time_frequency/tfr.py b/mne/time_frequency/tfr.py
 

+ index ce1c008ff..912e40f8c 100644
 

+ --- a/mne/time_frequency/tfr.py
 

+ +++ b/mne/time_frequency/tfr.py
 

+ @@ -248,7 +248,12 @@ def _cwt_gen(X, Ws, *, fsize=0, mode="same", decim=1, use_fft=True):
 

+              if use_fft:
 

+                  ret = ifft(fft_x * fft_Ws[ii])[:n_times + W.size - 1]
 

+              else:
 

+ -                ret = np.convolve(x, W, mode=mode)
 

+ +                # Work around multarray.correlate->OpenBLAS bug on ppc64le
 

+ +                # ret = np.correlate(x, W, mode=mode)
 

+ +                ret = (
 

+ +                    np.convolve(x, W.real, mode=mode) +
 

+ +                    1j * np.convolve(x, W.imag, mode=mode)
 

+ +                )
 

+  

+              # Center and decimate decomposition
 

+              if mode == 'valid':
 

+ diff --git a/requirements.txt b/requirements.txt
 

+ index f666856bc..20da23a48 100644
 

+ --- a/requirements.txt
 

+ +++ b/requirements.txt
 

+ @@ -9,7 +9,7 @@ h5io
 

+  packaging
 

+  pymatreader
 

+  qtpy
 

+ -PySide6!=6.3.0,!=6.4.0  # incompat with Matplotlib 3.6.1
 

+ +PySide6!=6.3.0,!=6.4.0,!=6.4.0.1  # incompat with Matplotlib 3.6.1 and qtpy
 

+  pyobjc-framework-Cocoa>=5.2.0; platform_system=="Darwin"
 

+  sip
 

+  scikit-learn
 

+ -- 

+ 2.37.3
 

+

file modified
+9 -10 
@@ -5,7 +5,7 @@ 
 

  # in setup.py for install_requires.
 

  

  Name:           python-mne
 

- Version:        1.2.0
 

+ Version:        1.2.1
 

  Release:        %autorelease
 

  Summary:        Magnetoencephalography (MEG) and Electroencephalography (EEG) data analysis
 

  
@@ -21,6 +21,12 @@ 
 

  # https://fedoraproject.org/wiki/Changes/EncourageI686LeafRemoval
 

  ExcludeArch:    %{ix86}
 

  

+ # BUG: Work around ppc64le bugs
 

+ # https://github.com/mne-tools/mne-python/pull/11284
 

+ #
 

+ # Rebased on 1.2.1
 

+ Patch:          0001-BUG-Work-around-ppc64le-bugs-11284.patch
 

+ 

  # The combination of an arched package with only noarch binary packages makes
 

  # it easier for us to detect arch-dependent test failures, since the tests will
 

  # always be run on every platform, and easier for us to skip failing tests if
 
@@ -109,7 +115,7 @@ 
 

  %description -n python3-mne %_description
 

  

  %prep
 

- %autosetup -n mne-python-%{version}
 

+ %autosetup -n mne-python-%{version} -p1
 

  

  # fix non-executable scripts
 

  sed -i -e '1{\@^#!/usr/bin/env python@d}' mne/commands/*.py
 
@@ -145,16 +151,9 @@ 
 

  # required for some tests
 

  mkdir subjects
 

  

- # One test failure on aarch64
 

- # https://github.com/mne-tools/mne-python/issues/10984
 

- k="${k-}${k+ and }not test_mxne_inverse_sure_synthetic[3-0.75-4-20-60-20]"
 

- # Two test failures on ppc64le
 

- # https://github.com/mne-tools/mne-python/issues/10985
 

- k="${k-}${k+ and }not test_csd_morlet"
 

- k="${k-}${k+ and }not test_time_frequency"
 

  # https://github.com/mne-tools/mne-python/blob/v1.0.3/tools/github_actions_test.sh#L7
 

  # skip tests that require network
 

- %pytest -k "${k-}" -m "not (slowtest or pgtest)" \
 

+ %pytest -m "not (slowtest or pgtest)" \
 

      --deselect mne/datasets/tests/test_datasets.py \
 

      --deselect mne/utils/tests/test_numerics.py

file modified
+1 -1 
@@ -1,1 +1,1 @@ 
 

- SHA512 (python-mne-1.2.0.tar.gz) = e5b36d298d27e13bc5edff28e8f30c72fc98d0ce6e38352e6a9264365421c89e7cd69213398d441d107c98423c8e71104442a1bb980b200c4bc49630d181b4c4
 

+ SHA512 (python-mne-1.2.1.tar.gz) = 9455a0c952803793b96637ebabe35471ed07357e907e21d08fc390f052c1dad452b0577cceaad994961d788298d74f731c6c20d75137328309047c69052e5017

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