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Cristiano Köhler
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Merge branch 'master' into enh/trial_by_trial_methods
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‎.github/workflows/CI.yml‎

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@@ -134,7 +134,7 @@ jobs:
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fail-fast: false
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matrix:
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# OS [ubuntu-latest, macos-latest, windows-latest]
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os: [macos-13,macos-14]
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os: [macos-14,macos-15]
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python-version: [3.12]
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steps:
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- name: Get current year-month
@@ -143,6 +143,17 @@ jobs:
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- uses: actions/[email protected]
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/[email protected]
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with:
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python-version: ${{ matrix.python-version }}
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check-latest: true
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cache: 'pip'
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cache-dependency-path: |
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**/requirements.txt
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**/requirements-extras.txt
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**/requirements-tests.txt
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- name: Get current hash (SHA) of the elephant_data repo
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id: elephant-data
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run: |
@@ -157,11 +168,11 @@ jobs:
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restore-keys: datasets-
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- name: Install dependencies
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shell: bash -l {0}
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run: |
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python --version
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pip install -e .[extras,tests]
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python -m pip install --upgrade pip
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pip install pytest-cov coveralls
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pip install -e .[extras,tests]
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- name: List packages
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shell: bash -l {0}
@@ -366,29 +377,24 @@ jobs:
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restore-keys: datasets-
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enableCrossOsArchive: true
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- uses: conda-incubator/setup-miniconda@d2e6a045a86077fb6cad6f5adf368e9076ddaa8d # corresponds to v3.1.0
380+
- uses: mamba-org/setup-micromamba@v2
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with:
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auto-update-conda: true
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python-version: ${{ matrix.python-version }}
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mamba-version: "*"
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channels: conda-forge
375-
channel-priority: true
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activate-environment: elephant
382+
create-args: python=${{ matrix.python-version }}
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environment-file: requirements/environment-tests.yml
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conda-remove-defaults: true
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init-shell: bash
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- name: Install dependencies
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shell: bash -el {0}
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run: |
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python --version
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mamba install -c conda-forge pytest pytest-cov coveralls mpi4py openmpi
390+
micromamba install -y -c conda-forge pytest pytest-cov coveralls mpi4py openmpi
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pip install -e .
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- name: List packages
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shell: bash -el {0}
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run: |
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pip list
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mamba list
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micromamba list
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python --version
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- name: Test with pytest
@@ -438,23 +444,20 @@ jobs:
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key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements-docs.txt') }}-${{ hashFiles('**/requirements-tutorials.txt') }}-${{ hashFiles('**/environment-docs.yml') }}
439445
-${{ hashFiles('**/CI.yml') }}-${{ steps.date.outputs.date }}
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441-
- uses: conda-incubator/setup-miniconda@d2e6a045a86077fb6cad6f5adf368e9076ddaa8d # corresponds to v3.1.0
447+
- uses: mamba-org/setup-micromamba@v2
442448
with:
443-
auto-update-conda: true
444-
python-version: ${{ matrix.python-version }}
445-
mamba-version: "*"
446-
activate-environment: elephant
449+
create-args: python=${{ matrix.python-version }}
447450
environment-file: requirements/environment.yml
448-
conda-remove-defaults: true
451+
init-shell: bash
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450453
- name: Install dependencies
451-
shell: bash -el {0} # enables conda incubator to activate environment
454+
shell: bash -el {0}
452455
run: |
453456
sudo apt-get update
454457
sudo apt install -y libopenmpi-dev openmpi-bin
455458
456-
mamba install -c conda-forge openmpi pandoc libstdcxx-ng # fix libstdc++.so.6: version for new scipy versions > 1.9.1
457-
mamba env update --file requirements/environment-docs.yml --name elephant
459+
micromamba install -y -c conda-forge openmpi pandoc libstdcxx-ng # fix libstdc++.so.6: version for new scipy versions > 1.9.1
460+
micromamba env update --file requirements/environment-docs.yml --name elephant
458461
python -m pip install --upgrade pip
459462
pip install -e .[extras,tutorials,docs]
460463
# run notebooks
@@ -464,7 +467,7 @@ jobs:
464467
shell: bash -el {0}
465468
run: |
466469
pip list
467-
mamba list
470+
micromamba list
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python --version
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- name: make html

‎.github/workflows/build_wheels.yml‎

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@@ -15,7 +15,7 @@ jobs:
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
18-
os: [ubuntu-20.04, windows-2019]
18+
os: [ubuntu-latest, windows-latest]
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steps:
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- uses: actions/checkout@v4

‎README.md‎

Lines changed: 9 additions & 7 deletions
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@@ -1,16 +1,18 @@
11
# Elephant - Electrophysiology Analysis Toolkit
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[![Coverage Status](https://coveralls.io/repos/github/NeuralEnsemble/elephant/badge.svg?branch=master)](https://coveralls.io/github/NeuralEnsemble/elephant?branch=master)
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[![Test Status](https://github.com/NeuralEnsemble/elephant/actions/workflows/CI.yml/badge.svg)](https://github.com/NeuralEnsemble/elephant/actions/workflows/CI.yml)
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[![Documentation Status](https://readthedocs.org/projects/elephant/badge/?version=latest)](https://elephant.readthedocs.io/en/latest/?badge=latest)
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[![![PyPi]](https://img.shields.io/pypi/v/elephant)](https://pypi.org/project/elephant/)
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[![Statistics](https://img.shields.io/pypi/dm/elephant)](https://seladb.github.io/StarTrack-js/#/preload?r=neuralensemble,elephant)
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[![Gitter](https://badges.gitter.im/python-elephant/community.svg)](https://gitter.im/python-elephant/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)
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[![![PyPi] Status](https://img.shields.io/pypi/v/elephant)](https://pypi.org/project/elephant/)
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[![DOI Latest Release](https://zenodo.org/badge/10311278.svg)](https://zenodo.org/badge/latestdoi/10311278)
9-
[![tests](https://github.com/NeuralEnsemble/elephant/actions/workflows/CI.yml/badge.svg)](https://github.com/NeuralEnsemble/elephant/actions/workflows/CI.yml)
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[![CII Best Practices](https://bestpractices.coreinfrastructure.org/projects/6191/badge)](https://bestpractices.coreinfrastructure.org/projects/6191)
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[![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu)
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[![Download Statistics](https://img.shields.io/pypi/dm/elephant)](https://seladb.github.io/StarTrack-js/#/preload?r=neuralensemble,elephant)<br>
9+
[![Chat on Gitter](https://badges.gitter.im/python-elephant/community.svg)](https://gitter.im/python-elephant/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)
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[![Follow me on Bluesky](https://img.shields.io/badge/Bluesky-0285FF?logo=bluesky&logoColor=fff&label=Follow%20me%20on&color=0285FF)](https://bsky.app/profile/pyelephant.bsky.social)
13-
[![Fosstodon](https://img.shields.io/badge/@elephant-6364FF?logo=mastodon&logoColor=fff&style=flat)](https://fosstodon.org/@elephant)
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[![Follow me on Fosstodon](https://img.shields.io/badge/@elephant-6364FF?logo=mastodon&logoColor=fff&style=flat)](https://fosstodon.org/@elephant)<br>
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[![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu)
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[![OpenSSF/CII Best Practices](https://bestpractices.coreinfrastructure.org/projects/6191/badge)](https://bestpractices.coreinfrastructure.org/projects/6191)
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[![JURSE Code Pick](https://img.shields.io/badge/JuRSE_Code_Pick-Nov_2025-blue)](https://www.fz-juelich.de/en/rse/community-initiatives/jurse-code-of-the-month/november-2025)
15+
![HiRSE Code Promo](https://img.shields.io/badge/Promo-8db427?label=HiRSE&labelColor=005aa0&link=https%3A%2F%2Fgo.fzj.de%2FCodePromo)
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*Elephant* package analyses all sorts of neurophysiological data:

‎elephant/test/test_signal_processing.py‎

Lines changed: 14 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -448,31 +448,33 @@ def test_butter_filter_type(self):
448448
# this by using an identity function for detrending
449449
filtered_noise = elephant.signal_processing.butter(
450450
noise, 250.0 * pq.Hz, None)
451-
_, psd = spsig.welch(filtered_noise.T, nperseg=1024, fs=1000.0,
452-
detrend=lambda x: x)
451+
_, psd = spsig.welch(filtered_noise.magnitude.T,
452+
nperseg=1024, fs=1000.0, detrend=lambda x: x)
453453
self.assertAlmostEqual(psd[0, 0], 0)
454454

455455
# test low-pass filtering: power at the highest frequency
456456
# should be almost zero
457457
filtered_noise = elephant.signal_processing.butter(
458458
noise, None, 250.0 * pq.Hz)
459-
_, psd = spsig.welch(filtered_noise.T, nperseg=1024, fs=1000.0)
459+
_, psd = spsig.welch(filtered_noise.magnitude.T, nperseg=1024,
460+
fs=1000.0)
460461
self.assertAlmostEqual(psd[0, -1], 0)
461462

462463
# test band-pass filtering: power at the lowest and highest frequencies
463464
# should be almost zero
464465
filtered_noise = elephant.signal_processing.butter(
465466
noise, 200.0 * pq.Hz, 300.0 * pq.Hz)
466-
_, psd = spsig.welch(filtered_noise.T, nperseg=1024, fs=1000.0,
467-
detrend=lambda x: x)
467+
_, psd = spsig.welch(filtered_noise.magnitude.T, nperseg=1024,
468+
fs=1000.0, detrend=lambda x: x)
468469
self.assertAlmostEqual(psd[0, 0], 0)
469470
self.assertAlmostEqual(psd[0, -1], 0)
470471

471472
# test band-stop filtering: power at the intermediate frequency
472473
# should be almost zero
473474
filtered_noise = elephant.signal_processing.butter(
474475
noise, 400.0 * pq.Hz, 100.0 * pq.Hz)
475-
_, psd = spsig.welch(filtered_noise.T, nperseg=1024, fs=1000.0)
476+
_, psd = spsig.welch(filtered_noise.magnitude.T, nperseg=1024,
477+
fs=1000.0)
476478
self.assertAlmostEqual(psd[0, 256], 0)
477479

478480
def test_butter_filter_function(self):
@@ -493,17 +495,20 @@ def test_butter_filter_function(self):
493495
'lowpass_frequency': None, 'filter_function': 'filtfilt'}
494496
filtered_noise = elephant.signal_processing.butter(**kwds)
495497
_, psd_filtfilt = spsig.welch(
496-
filtered_noise.T, nperseg=1024, fs=1000.0, detrend=lambda x: x)
498+
filtered_noise.magnitude.T, nperseg=1024, fs=1000.0,
499+
detrend=lambda x: x)
497500

498501
kwds['filter_function'] = 'lfilter'
499502
filtered_noise = elephant.signal_processing.butter(**kwds)
500503
_, psd_lfilter = spsig.welch(
501-
filtered_noise.T, nperseg=1024, fs=1000.0, detrend=lambda x: x)
504+
filtered_noise.magnitude.T, nperseg=1024, fs=1000.0,
505+
detrend=lambda x: x)
502506

503507
kwds['filter_function'] = 'sosfiltfilt'
504508
filtered_noise = elephant.signal_processing.butter(**kwds)
505509
_, psd_sosfiltfilt = spsig.welch(
506-
filtered_noise.T, nperseg=1024, fs=1000.0, detrend=lambda x: x)
510+
filtered_noise.magnitude.T, nperseg=1024, fs=1000.0,
511+
detrend=lambda x: x)
507512

508513
self.assertAlmostEqual(psd_filtfilt[0, 0], psd_lfilter[0, 0])
509514
self.assertAlmostEqual(psd_filtfilt[0, 0], psd_sosfiltfilt[0, 0])

‎elephant/test/test_spectral.py‎

Lines changed: 7 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -97,9 +97,13 @@ def test_welch_psd_behavior(self):
9797
for key, val in params.items():
9898
freqs, psd = elephant.spectral.welch_psd(
9999
data, len_segment=1000, overlap=0, **{key: val})
100-
freqs_spsig, psd_spsig = spsig.welch(np.rollaxis(data, 0, len(
101-
data.shape)), fs=1 / sampling_period, nperseg=1000,
102-
noverlap=0, **{key: val})
100+
freqs_spsig, psd_spsig = spsig.welch(
101+
np.rollaxis(data.magnitude, 0, len(data.shape)),
102+
fs=1 / sampling_period,
103+
nperseg=1000,
104+
noverlap=0,
105+
**{key: val}
106+
)
103107
self.assertTrue(
104108
(freqs == freqs_spsig).all() and (
105109
psd == psd_spsig).all())

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