add author and license notes, fix links, remove alpha

.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: |

README.rst

@@ -46,12 +46,6 @@ For documentation, see the:
 `Preprocessing Pipeline (PREP) <https://doi.org/10.3389/fninf.2015.00016>`_
 for EEG data, working with `MNE-Python <https://mne.tools>`_.
 
-**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
 =============

examples/run_full_prep.py

@@ -14,12 +14,8 @@
 .. currentmodule:: pyprep
 """  # noqa: D205 D400
 
-# Authors: Aamna Lawrence <[email protected]>
-#          Adam Li <[email protected]>
-#          Victor Xiang <[email protected]>
-#
-# License: MIT
-#
+# Authors: The PyPREP developers
+# SPDX-License-Identifier: MIT
 
 ###############################################################################
 #

examples/run_ransac.py

@@ -9,10 +9,8 @@
 .. currentmodule:: pyprep
 """  # noqa: D205 D400
 
-# Authors: Yorguin Mantilla <[email protected]>
-#
-# 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.

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

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

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
 

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

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

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
 

tests/__init__.py

@@ -1 +1,4 @@
-"""Initilialize testing of pyprep modules."""
+"""Initilialize testing of PyPREP modules."""
+
+# Authors: The PyPREP developers
+# SPDX-License-Identifier: MIT

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

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
 

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

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

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

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