diff --git a/.github/workflows/python_tests.yml b/.github/workflows/python_tests.yml index 744c383..73c73d2 100644 --- a/.github/workflows/python_tests.yml +++ b/.github/workflows/python_tests.yml @@ -54,7 +54,7 @@ jobs: - name: Install MNE-Python (development version) if: matrix.mne-version == 'mne-main' run: | - pip install git+https://github.com/mne-tools/mne-python.git@main + pip install --upgrade https://github.com/mne-tools/mne-python/archive/refs/heads/main.zip - name: Check installed versions run: | diff --git a/README.rst b/README.rst index 6867504..835c7a6 100644 --- a/README.rst +++ b/README.rst @@ -46,12 +46,6 @@ For documentation, see the: `Preprocessing Pipeline (PREP) `_ for EEG data, working with `MNE-Python `_. -**ALPHA SOFTWARE.** -**This package is currently in its early stages of iteration.** -**It may change both its internals or its user-facing API in the near future.** -**Any feedback and ideas on how to improve either of these is welcome!** -**Use this software at your own risk.** - Installation ============ @@ -75,13 +69,12 @@ For installing the **latest (development)** version of ``pyprep``, call: .. code-block:: Text - pip install git+https://github.com/sappelhoff/pyprep.git@main - + pip install --upgrade https://github.com/sappelhoff/pyprep/archive/refs/heads/main.zip Both the *stable* and the *latest* installation will additionally install all required dependencies automatically. The dependencies are defined in the ``pyproject.toml`` file under the -``project.optional-dependencies`` section. +``dependencies`` and ``project.optional-dependencies`` sections. Contributions ============= diff --git a/examples/run_full_prep.py b/examples/run_full_prep.py index 5ed9b50..7d704b9 100644 --- a/examples/run_full_prep.py +++ b/examples/run_full_prep.py @@ -14,12 +14,8 @@ .. currentmodule:: pyprep """ # noqa: D205 D400 -# Authors: Aamna Lawrence -# Adam Li -# Victor Xiang -# -# License: MIT -# +# Authors: The PyPREP developers +# SPDX-License-Identifier: MIT ############################################################################### # diff --git a/examples/run_ransac.py b/examples/run_ransac.py index 31dde8a..6eed304 100644 --- a/examples/run_ransac.py +++ b/examples/run_ransac.py @@ -9,10 +9,8 @@ .. currentmodule:: pyprep """ # noqa: D205 D400 -# Authors: Yorguin Mantilla -# -# License: MIT -# Based On: use_noisy_module.py +# Authors: The PyPREP developers +# SPDX-License-Identifier: MIT ############################################################################### # First we import what we need for this example. diff --git a/pyprep/__init__.py b/pyprep/__init__.py index ed9cb23..55b0c95 100644 --- a/pyprep/__init__.py +++ b/pyprep/__init__.py @@ -1,5 +1,8 @@ """Initialize PyPREP.""" +# Authors: The PyPREP developers +# SPDX-License-Identifier: MIT + import pyprep.ransac as ransac # noqa: F401 from pyprep.find_noisy_channels import NoisyChannels # noqa: F401 from pyprep.prep_pipeline import PrepPipeline # noqa: F401 diff --git a/pyprep/find_noisy_channels.py b/pyprep/find_noisy_channels.py index 4be9acf..65431d9 100644 --- a/pyprep/find_noisy_channels.py +++ b/pyprep/find_noisy_channels.py @@ -1,5 +1,8 @@ """finds bad channels.""" +# Authors: The PyPREP developers +# SPDX-License-Identifier: MIT + import mne import numpy as np from mne.utils import check_random_state, logger diff --git a/pyprep/prep_pipeline.py b/pyprep/prep_pipeline.py index 94a375a..099391e 100644 --- a/pyprep/prep_pipeline.py +++ b/pyprep/prep_pipeline.py @@ -1,5 +1,8 @@ """Module for PREP pipeline.""" +# Authors: The PyPREP developers +# SPDX-License-Identifier: MIT + import mne from mne.utils import check_random_state diff --git a/pyprep/ransac.py b/pyprep/ransac.py index c73ff90..f2f96ab 100644 --- a/pyprep/ransac.py +++ b/pyprep/ransac.py @@ -1,5 +1,8 @@ """RANSAC bad channel identification.""" +# Authors: The PyPREP developers +# SPDX-License-Identifier: MIT + import mne import numpy as np from mne.channels.interpolation import _make_interpolation_matrix diff --git a/pyprep/removeTrend.py b/pyprep/removeTrend.py index 155e265..0b9e345 100644 --- a/pyprep/removeTrend.py +++ b/pyprep/removeTrend.py @@ -1,5 +1,8 @@ """High-pass filter and locally detrend the EEG signal.""" +# Authors: The PyPREP developers +# SPDX-License-Identifier: MIT + import logging import mne diff --git a/pyprep/utils.py b/pyprep/utils.py index 8cf27a5..59f49b3 100644 --- a/pyprep/utils.py +++ b/pyprep/utils.py @@ -1,5 +1,8 @@ """Module contains frequently used functions dealing with channel lists.""" +# Authors: The PyPREP developers +# SPDX-License-Identifier: MIT + import math from cmath import sqrt diff --git a/tests/__init__.py b/tests/__init__.py index 688b19b..b9a2299 100644 --- a/tests/__init__.py +++ b/tests/__init__.py @@ -1 +1,4 @@ -"""Initilialize testing of pyprep modules.""" +"""Initilialize testing of PyPREP modules.""" + +# Authors: The PyPREP developers +# SPDX-License-Identifier: MIT diff --git a/tests/conftest.py b/tests/conftest.py index 37eed85..d9aadd9 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -1,5 +1,8 @@ """Configure tests.""" +# Authors: The PyPREP developers +# SPDX-License-Identifier: MIT + import mne import numpy as np import pytest diff --git a/tests/test_find_noisy_channels.py b/tests/test_find_noisy_channels.py index 15cf35a..be2e6c1 100644 --- a/tests/test_find_noisy_channels.py +++ b/tests/test_find_noisy_channels.py @@ -1,5 +1,8 @@ """Test the find_noisy_channels module.""" +# Authors: The PyPREP developers +# SPDX-License-Identifier: MIT + import numpy as np import pytest diff --git a/tests/test_matprep_compare.py b/tests/test_matprep_compare.py index 2112fde..808deea 100644 --- a/tests/test_matprep_compare.py +++ b/tests/test_matprep_compare.py @@ -1,5 +1,8 @@ """Compare PyPREP results to MATLAB PREP.""" +# Authors: The PyPREP developers +# SPDX-License-Identifier: MIT + from urllib.request import urlopen import mne diff --git a/tests/test_prep_pipeline.py b/tests/test_prep_pipeline.py index f6a7755..d0807ff 100644 --- a/tests/test_prep_pipeline.py +++ b/tests/test_prep_pipeline.py @@ -1,5 +1,8 @@ """Test the full PREP pipeline.""" +# Authors: The PyPREP developers +# SPDX-License-Identifier: MIT + import matplotlib.pyplot as plt import mne import numpy as np diff --git a/tests/test_removeTrend.py b/tests/test_removeTrend.py index a447d6e..af553e7 100644 --- a/tests/test_removeTrend.py +++ b/tests/test_removeTrend.py @@ -1,5 +1,8 @@ """Test remove trend.""" +# Authors: The PyPREP developers +# SPDX-License-Identifier: MIT + import numpy as np import pyprep.removeTrend as removeTrend diff --git a/tests/test_utils.py b/tests/test_utils.py index c395cdf..97a7806 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -1,5 +1,8 @@ """Test various helper functions.""" +# Authors: The PyPREP developers +# SPDX-License-Identifier: MIT + import numpy as np import pytest