Rename LORIS electrophysiology chunker

.github/labeler.yml

@@ -12,7 +12,7 @@
 
 "Package: EEG chunker":
 - changed-files:
-  - any-glob-to-any-file: 'python/loris_eeg_chunker/**'
+  - any-glob-to-any-file: 'python/loris_ephys_chunker/**'
 
 "Package: Utilities":
 - changed-files:

pyproject.toml

@@ -25,9 +25,9 @@ dependencies = [
     "scipy",
     "sqlalchemy>=2.0.0",
     "virtualenv",
-    "loris-bids-reader @ {root:uri}/python/loris_bids_reader",
-    "loris-eeg-chunker @ {root:uri}/python/loris_eeg_chunker",
-    "loris-utils       @ {root:uri}/python/loris_utils",
+    "loris-bids-reader   @ {root:uri}/python/loris_bids_reader",
+    "loris-ephys-chunker @ {root:uri}/python/loris_ephys_chunker",
+    "loris-utils         @ {root:uri}/python/loris_utils",
 ]
 
 [project.optional-dependencies]
@@ -53,9 +53,9 @@ packages = [
 members = ["python/loris_*"]
 
 [tool.uv.sources]
-loris_bids_reader = { workspace = true }
-loris_eeg_chunker = { workspace = true }
-loris_utils       = { workspace = true }
+loris_bids_reader   = { workspace = true }
+loris_ephys_chunker = { workspace = true }
+loris_utils         = { workspace = true }
 
 [tool.ruff]
 src = ["python"]
@@ -94,11 +94,11 @@ include = [
     "python/scripts/import_dicom_study.py",
     "python/scripts/summarize_dicom_study.py",
     "python/loris_bids_reader",
-    "python/loris_eeg_chunker",
+    "python/loris_ephys_chunker",
     "python/loris_utils",
 ]
 exclude = [
-    "python/loris_eeg_chunker/src/loris_eeg_chunker/protocol_buffers",
+    "python/loris_ephys_chunker/src/loris_ephys_chunker/protocol_buffers",
 ]
 typeCheckingMode = "strict"
 reportMissingTypeStubs = "none"

python/loris_ephys_chunker/README.md

@@ -0,0 +1,35 @@
+# LORIS electrophysiology chunker
+
+## Description
+
+A set of scripts to chunk EEG and MEG data in smaller bits for visualization in the LORIS electrophysiology browser.
+
+## Installation
+
+The LORIS electrophysiology chunker can be installed as a Python package by using the following command from the root LORIS Python directory:
+
+```sh
+pip install python/loris_ephys_chunker
+```
+
+## Scripts
+
+The LORIS electrophysiology chunker currently supports the following file types with the following scripts:
+- EEG EDF: `edf-to-chunks`
+- EEG EEGLAB: `eeglab-to-chunks`
+- MEG CTF: `ctf-to-chunks`
+
+## Use
+
+The LORIS electrophysiology chunker can be used using the following command:
+
+```sh
+script path/to/acquisition -d path/to/destination/dir
+```
+
+## Credits
+
+These scripts were extracted on July 8th, 2019 from the master branch of the following Github repository:
+https://github.com/ArminTaheri/react-series-data-viewer.
+
+Author: Armin Taheri; armin.taheri@mcgill.ca

python/loris_eeg_chunker/pyproject.toml → python/loris_ephys_chunker/pyproject.toml

@@ -1,7 +1,7 @@
 [project]
-name = "loris-eeg-chunker"
+name = "loris-ephys-chunker"
 version = "27.0.0"
-description = "The LORIS EEG chunker"
+description = "The LORIS electrophysiology chunker"
 readme = "README.md"
 license = "GPL-3.0-or-later"
 requires-python = ">= 3.11"
@@ -15,16 +15,16 @@ dependencies = [
 ]
 
 [project.scripts]
-ctf-to-chunks    = "loris_eeg_chunker.scripts.ctf_to_chunks:main"
-edf-to-chunks    = "loris_eeg_chunker.scripts.edf_to_chunks:main"
-eeglab-to-chunks = "loris_eeg_chunker.scripts.eeglab_to_chunks:main"
+ctf-to-chunks    = "loris_ephys_chunker.scripts.ctf_to_chunks:main"
+edf-to-chunks    = "loris_ephys_chunker.scripts.edf_to_chunks:main"
+eeglab-to-chunks = "loris_ephys_chunker.scripts.eeglab_to_chunks:main"
 
 [build-system]
 requires = ["hatchling"]
 build-backend = "hatchling.build"
 
 [tool.hatch.build.targets.wheel]
-packages = ["src/loris_eeg_chunker"]
+packages = ["src/loris_ephys_chunker"]
 
 [tool.ruff]
 extend = "../../pyproject.toml"

python/loris_eeg_chunker/src/loris_eeg_chunker/chunking.py → python/loris_ephys_chunker/src/loris_ephys_chunker/chunking.py

@@ -11,7 +11,7 @@
 from mne.io import BaseRaw
 from scipy import signal
 
-from loris_eeg_chunker.protocol_buffers import chunk_pb2 as chunk_pb
+from loris_ephys_chunker.protocol_buffers import chunk_pb2 as chunk_pb
 
 ChannelArray = npt.NDArray[np.float64]
 

python/loris_eeg_chunker/src/loris_eeg_chunker/scripts/ctf_to_chunks.py → python/loris_ephys_chunker/src/loris_ephys_chunker/scripts/ctf_to_chunks.py

@@ -8,7 +8,7 @@
 import mne.io
 from mne.io.ctf import RawCTF
 
-from loris_eeg_chunker.chunking import write_chunk_directory  # type: ignore
+from loris_ephys_chunker.chunking import write_chunk_directory  # type: ignore
 
 
 def load_channels(path: Path) -> RawCTF:

python/loris_eeg_chunker/src/loris_eeg_chunker/scripts/edf_to_chunks.py → python/loris_ephys_chunker/src/loris_ephys_chunker/scripts/edf_to_chunks.py

@@ -10,7 +10,7 @@
 import mne.io.edf.edf as mne_edf
 from mne.io.edf.edf import RawEDF
 
-from loris_eeg_chunker.chunking import write_chunk_directory
+from loris_ephys_chunker.chunking import write_chunk_directory
 
 
 def load_channels(exclude: list[str]) -> Callable[[Path], RawEDF]:

python/loris_eeg_chunker/src/loris_eeg_chunker/scripts/eeglab_to_chunks.py → python/loris_ephys_chunker/src/loris_ephys_chunker/scripts/eeglab_to_chunks.py

@@ -9,7 +9,7 @@
 import mne.io.eeglab.eeglab as mne_eeglab
 from mne.io.eeglab.eeglab import RawEEGLAB
 
-from loris_eeg_chunker.chunking import write_chunk_directory
+from loris_ephys_chunker.chunking import write_chunk_directory
 
 
 def load_channels(path: Path) -> RawEEGLAB:

test/pyrightconfig.json

@@ -1,6 +1,6 @@
 {
     "include": ["../python"],
-    "exclude": ["../python/loris_eeg_chunker/protocol_buffers"],
+    "exclude": ["../python/loris_ephys_chunker/protocol_buffers"],
     "typeCheckingMode": "off",
     "reportDeprecated": "warning",
     "reportAbstractUsage": "error",