add some CI ignores; finish package rename (#23)

Author: drammock

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 
 [project]
-name = "ilabs_streamsync"
+name = "streamsync"
 authors = [
   { name = "Daniel McCloy", email = "dan@mccloy.info" },
 ]
@@ -21,11 +21,8 @@ classifiers = [
   "Programming Language :: Python",
   "Programming Language :: Python :: 3",
   "Programming Language :: Python :: 3 :: Only",
-  "Programming Language :: Python :: 3.8",
-  "Programming Language :: Python :: 3.9",
-  "Programming Language :: Python :: 3.10",
-  "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
   "Topic :: Scientific/Engineering",
   "Typing :: Typed",
 ]
@@ -50,15 +47,15 @@ docs = [
 ]
 
 [project.urls]
-Homepage = "https://github.com/ilabsbrainteam/ilabs_streamsync"
-"Bug Tracker" = "https://github.com/ilabsbrainteam/ilabs_streamsync/issues"
-Discussions = "https://github.com/ilabsbrainteam/ilabs_streamsync/discussions"
-Changelog = "https://github.com/ilabsbrainteam/ilabs_streamsync/releases"
+Homepage = "https://github.com/ilabsbrainteam/streamsync"
+"Bug Tracker" = "https://github.com/ilabsbrainteam/streamsync/issues"
+Discussions = "https://github.com/ilabsbrainteam/streamsync/discussions"
+Changelog = "https://github.com/ilabsbrainteam/streamsync/releases"
 
 
 [tool.hatch]
 version.source = "vcs"
-build.hooks.vcs.version-file = "src/ilabs_streamsync/_version.py"
+build.hooks.vcs.version-file = "src/streamsync/_version.py"
 
 [tool.hatch.envs.default]
 features = ["test"]
@@ -79,15 +76,15 @@ testpaths = [
 
 
 [tool.coverage]
-run.source = ["ilabs_streamsync"]
+run.source = ["streamsync"]
 report.exclude_also = [
   '\.\.\.',
   'if typing.TYPE_CHECKING:',
 ]
 
 [tool.mypy]
 files = ["src", "tests"]
-python_version = "3.8"
+python_version = "3.12"
 warn_unused_configs = true
 strict = true
 enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"]
@@ -96,7 +93,7 @@ disallow_untyped_defs = false
 disallow_incomplete_defs = false
 
 [[tool.mypy.overrides]]
-module = "ilabs_streamsync.*"
+module = "streamsync.*"
 disallow_untyped_defs = true
 disallow_incomplete_defs = true
 
@@ -135,15 +132,15 @@ ignore = [
 ]
 isort.required-imports = ["from __future__ import annotations"]
 # Uncomment if using a _compat.typing backport
-# typing-modules = ["ilabs_streamsync._compat.typing"]
+# typing-modules = ["streamsync._compat.typing"]
 
 [tool.ruff.lint.per-file-ignores]
 "tests/**" = ["T20"]
 "noxfile.py" = ["T20"]
 
 
 [tool.pylint]
-py-version = "3.8"
+py-version = "3.12"
 ignore-paths = [".*/_version.py"]
 reports.output-format = "colorized"
 similarities.ignore-imports = "yes"

src/ilabs_streamsync/example_script.py

@@ -7,6 +7,6 @@
 from __future__ import annotations
 
 # from ._version import version as __version__
-from .streamsync import StreamSync
+from .streamsync import StreamSync, extract_audio_from_video
 
-__all__ = ["__version__", "StreamSync"]
+__all__ = ["__version__", "StreamSync", "extract_audio_from_video"]

src/ilabs_streamsync/streamsync.py

@@ -0,0 +1,37 @@
+from __future__ import annotations
+
+import mne
+
+from streamsync import StreamSync, extract_audio_from_video
+
+# load an MNE raw file
+raw = mne.io.read_raw("")
+cam1 = "path/to/video"
+flux1 = mne.io.read_raw("")
+my_events = []
+
+
+subjects = ["146a", "222b"]
+
+for subj in subjects:
+    # MEG data from SQUID
+    ss = StreamSync(raw, "STIM001")
+    # audio from camera
+    audio1 = extract_audio_from_video(cam1, channel=2)
+    ss.add_stream(audio1, channel=1)
+    # MEG data from FLUX
+    ss.add_stream(flux1, channel=127)
+    # synchronize
+    result = ss.do_syncing()
+    # plot (to verify good sync)
+    fig = ss.plot_sync()
+    fig.savefig(...)  # optional
+    # add camera events to SQUID raw as Annotations
+    annot = ss.add_camera_events(my_events)
+    raw.set_annotations(annot)
+    if result < 0.7:
+        write_log_msg(f"subj {subj} had bad pulse syncing")  # noqa: F821
+        continue
+
+    # apply maxfilter
+    # do ICA

src/ilabs_streamsync/__init__.py src/streamsync/__init__.pysrc/ilabs_streamsync/__init__.py renamed to src/streamsync/__init__.py

@@ -0,0 +1,74 @@
+from __future__ import annotations
+
+import os
+
+import matplotlib.pyplot as plt
+import mne
+import numpy as np
+from numpy.typing import ArrayLike
+
+type Stream = mne.io.BaseRaw | ArrayLike
+type Channel = str | int
+type PathLike = str | bytes | os.PathLike
+
+
+class StreamSync:
+    """Synchronize two data streams.
+
+    Inputs: `mne.io.Raw` files, audio files (TODO which formats?),
+    and additional camera events.
+
+    Outputs: `mne.Annotations` object created from the camera events and
+    time-warped to the timescale of the `Raw`.
+    """
+
+    def __init__(self, reference_object: Stream, pulse_channel: Channel) -> None:
+        self.ref_stream: ArrayLike = reference_object.get_chan(pulse_channel)
+        self.sfreq: float = reference_object.info["sfreq"]  # Hz
+        self.streams: list[Stream] = []
+
+    def add_camera_events(self, events: ArrayLike) -> mne.Annotations:  # noqa: ARG002
+        return mne.Annotations([], [], [])
+
+    def add_stream(
+        self,
+        stream: Stream,
+        channel: Channel,
+        events: ArrayLike | None = None,  # noqa: ARG002
+    ) -> StreamSync:
+        """Add a new ``Raw`` or video stream, optionally with events.
+
+        stream : Raw | wav
+            An audio or FIF stream.
+        channel : str | int | None
+            Which channel of `stream` contains the sync pulse sequence.
+        events : array-like | None
+            Events associated with the stream. TODO: should they be integer sample
+            numbers? Timestamps? Do we support both?
+        """
+        pulses = self._extract_pulse_sequence_from_stream(stream, channel=channel)
+        self.streams.append(pulses)
+        return self
+
+    def _extract_pulse_sequence_from_stream(
+        self,
+        stream: Stream,  # noqa: ARG002
+        channel: Channel,  # noqa: ARG002
+    ) -> ArrayLike:
+        # TODO triage based on input type (e.g., if it's a Raw, pull out a stim chan,
+        # if it's audio, just add it as-is)
+        return np.array([])  # fake return
+
+    def do_syncing(self) -> float:
+        """Synchronize all streams with the reference stream."""
+        # TODO (waves hands) do the hard part.
+        # TODO spit out a report of correlation/association between all pairs of streams
+        return 0.0
+
+    def plot_sync(self) -> plt.figure.Figure:
+        return plt.figure.Figure()
+
+
+def extract_audio_from_video(path_to_video: PathLike, channel: Channel) -> ArrayLike:  # noqa: ARG001
+    """Path can be a regex or glob to allow batch processing."""
+    return np.array([])  # fake return

src/ilabs_streamsync/_version.pyi src/streamsync/_version.pyisrc/ilabs_streamsync/_version.pyi renamed to src/streamsync/_version.pyi

@@ -2,7 +2,7 @@
 
 import importlib.metadata
 
-import ilabs_streamsync as m
+import streamsync as m
 
 
 def test_version():