diff --git a/README.md b/README.md index 113b8cd..21d369a 100644 --- a/README.md +++ b/README.md @@ -40,13 +40,13 @@ https://doi.org/10.6084/m9.figshare.19705522 ## Contribution Pypi Release checklist: -Edit the version number in `setup.py`, and add release notes in `release_notes.md` +- Edit the version number in `setup.py`, and add release notes in `release_notes.md` ```shell flake8 -tag=vX.Y.Z +tag=X.Y.Z git tag -a $tag git push origin %tag ``` -Create new release with tag vX.Y.Z (will automatically publish to PyPI) +Create new release with tag X.Y.Z (will automatically publish to PyPI) diff --git a/release_notes.md b/release_notes.md index 8790b38..c1c1dee 100644 --- a/release_notes.md +++ b/release_notes.md @@ -1,4 +1,7 @@ # 1.0.0 +## 1.0.1 2024-05-29: support for waveform extraction on non-standard electrode layouts + - bugfix waveform extraction: the probe channel layout is inferred from the spikeglx metadata by default + - bugfix waveform extraction: the channel neighnourhood fill value is the last channel index + 1 by default instead of 384 ## 1.0.0 2024-04-22 - Functionalities to check and mitigate saturation in neuropixel recordings - `spikeglx.Reader` has a `range_volts` method to get the saturating voltage value for a given type of probe diff --git a/setup.py b/setup.py index 5077817..42d4401 100644 --- a/setup.py +++ b/setup.py @@ -8,7 +8,7 @@ setuptools.setup( name="ibl-neuropixel", - version="1.0.0", + version="1.0.1", author="The International Brain Laboratory", description="Collection of tools for Neuropixel 1.0 and 2.0 probes data", long_description=long_description, diff --git a/src/ibldsp/waveform_extraction.py b/src/ibldsp/waveform_extraction.py index c2f583e..ee9fb79 100644 --- a/src/ibldsp/waveform_extraction.py +++ b/src/ibldsp/waveform_extraction.py @@ -6,7 +6,6 @@ from numpy.lib.format import open_memmap from joblib import Parallel, delayed, cpu_count -import neuropixel import spikeglx from ibldsp.voltage import detect_bad_channels, interpolate_bad_channels, car from ibldsp.fourier import fshift diff --git a/src/spikeglx.py b/src/spikeglx.py index f851a0c..6045263 100644 --- a/src/spikeglx.py +++ b/src/spikeglx.py @@ -70,7 +70,7 @@ def __init__( """ self.ignore_warnings = ignore_warnings sglx_file = Path(sglx_file) - meta_file = meta_file or _get_companion_file(sglx_file, '.meta') + meta_file = meta_file or _get_companion_file(sglx_file, '.meta') # only used if MTSCOMP compressed self.ch_file = ch_file diff --git a/src/tests/unit/cpu/test_spikeglx.py b/src/tests/unit/cpu/test_spikeglx.py index 75d35a8..b91ffd4 100644 --- a/src/tests/unit/cpu/test_spikeglx.py +++ b/src/tests/unit/cpu/test_spikeglx.py @@ -629,14 +629,13 @@ def test_get_companion_file(self): self.assertEqual(meta_file, spikeglx._get_companion_file(sglx_file, '.meta')) with tempfile.TemporaryDirectory() as td: - sglx_file = Path(td) / f"sample3A_g0_t0.imec.ap.bin" - meta_file_ok = Path(td) / f"sample3A_g0_t0.imec.ap.meta" + sglx_file = Path(td) / "sample3A_g0_t0.imec.ap.bin" + meta_file_ok = Path(td) / "sample3A_g0_t0.imec.ap.meta" meta_file = Path(td) / f"sample3A_g0_t0.imec.ap.{str(uuid.uuid4())}.meta" meta_file.touch() meta_file_ok.touch() self.assertEqual(meta_file_ok, spikeglx._get_companion_file(sglx_file, '.meta')) - def test_read_flat_binary_float32(self): # here we expect no scaling to V applied and no sync trace as the format is float32 kwargs = dict(ns=60000, nc=384, fs=30000, dtype=np.float32)