Merge pull request #106 from cbrnr/gha

Run tests with GitHub Action

.github/workflows/test.yml

@@ -0,0 +1,38 @@
+name: Test
+
+on: [push, pull_request]
+
+jobs:
+  style:
+    name: Check style
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: chartboost/ruff-action@v1
+    - uses: chartboost/ruff-action@v1
+      with:
+        args: 'format --check'
+
+  test:
+    needs: style
+    strategy:
+      matrix:
+        python-version: ['3.9', '3.10', '3.11', '3.12']
+    name: Run tests (Python ${{ matrix.python-version }})
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Build sdist and wheel
+      run: |
+        pip install build
+        python -m build
+    - name: Install wheel
+      run: pip install "$(pwd)/$(echo dist/pyxdf*.whl)[dev]"
+    - name: Run tests
+      run: |
+        git clone https://github.com/xdf-modules/example-files.git
+        pip install pytest
+        pytest

pyxdf/examples/playback_lsl.py

@@ -1,11 +1,12 @@
 import argparse
-import time
 import sys
-from typing import List, Optional
+import time
 from dataclasses import dataclass
+from typing import List, Optional
 
 import numpy as np
 import pylsl
+
 import pyxdf
 
 
@@ -53,22 +54,33 @@ class Streamer:
 
 
 class LSLPlaybackClock:
-    def __init__(self, rate: float = 1.0, loop_time: float = 0.0, max_sample_rate: Optional[float] = None):
+    def __init__(
+        self,
+        rate: float = 1.0,
+        loop_time: float = 0.0,
+        max_sample_rate: Optional[float] = None,
+    ):
         if rate != 1.0:
-            print("WARNING!! rate != 1.0; It is impossible to synchronize playback streams "
-                  "with real time streams.")
+            print(
+                "WARNING!! rate != 1.0; It is impossible to synchronize playback streams "
+                "with real time streams."
+            )
         self.rate: float = rate  # Maximum rate is loop_time / avg_update_interval, whatever that might be.
         self._boundary = loop_time
         self._max_srate = max_sample_rate
         decr = (1 / self._max_srate) if self._max_srate else 2 * sys.float_info.epsilon
         self._wall_start: float = pylsl.local_clock() - decr / 2
         self._file_read_s: float = 0  # File read header in seconds
-        self._prev_file_read_s: float = 0  # File read header in seconds for previous iteration
+        self._prev_file_read_s: float = (
+            0  # File read header in seconds for previous iteration
+        )
         self._n_loop: int = 0
 
     def reset(self, reset_file_position: bool = False) -> None:
         decr = (1 / self._max_srate) if self._max_srate else 2 * sys.float_info.epsilon
-        self._wall_start = pylsl.local_clock() - decr / 2 - self._file_read_s / self.rate
+        self._wall_start = (
+            pylsl.local_clock() - decr / 2 - self._file_read_s / self.rate
+        )
         self._n_loop = 0
         if reset_file_position:
             self._file_read_s = 0
@@ -117,8 +129,13 @@ def sleep(self, duration: Optional[float] = None) -> None:
         time.sleep(duration / self.rate)
 
 
-def main(fname: str, playback_speed: float = 1.0, loop: bool = True, wait_for_consumer: bool = False):
-    streams, header = pyxdf.load_xdf(fname)
+def main(
+    fname: str,
+    playback_speed: float = 1.0,
+    loop: bool = True,
+    wait_for_consumer: bool = False,
+):
+    streams, _ = pyxdf.load_xdf(fname)
 
     # First iterate over all streams to calculate some globals.
     xdf_t0 = np.inf
@@ -140,20 +157,32 @@ def main(fname: str, playback_speed: float = 1.0, loop: bool = True, wait_for_co
         tvec = strm["time_stamps"]
         srate = float(strm["info"]["nominal_srate"][0])
         if len(tvec) > 0:
-            new_info: pylsl.StreamInfo = _create_info_from_xdf_stream_header(strm["info"])
+            new_info: pylsl.StreamInfo = _create_info_from_xdf_stream_header(
+                strm["info"]
+            )
             new_outlet: pylsl.StreamOutlet = pylsl.StreamOutlet(new_info)
-            streamers.append(Streamer(strm_ix, new_info.name(), tvec - xdf_t0, new_info, new_outlet, srate))
+            streamers.append(
+                Streamer(
+                    strm_ix, new_info.name(), tvec - xdf_t0, new_info, new_outlet, srate
+                )
+            )
 
     # Create timer to manage playback.
-    timer = LSLPlaybackClock(rate=playback_speed, loop_time=wrap_dur if loop else None, max_sample_rate=max_rate)
+    timer = LSLPlaybackClock(
+        rate=playback_speed,
+        loop_time=wrap_dur if loop else None,
+        max_sample_rate=max_rate,
+    )
     read_heads = {_.name: 0 for _ in streamers}
     b_push = not wait_for_consumer  # A flag to indicate we can push samples.
     try:
         while True:
             if not b_push:
                 # We are looking for consumers.
                 time.sleep(0.01)
-                have_consumers = [streamer.outlet.have_consumers() for streamer in streamers]
+                have_consumers = [
+                    streamer.outlet.have_consumers() for streamer in streamers
+                ]
                 # b_push = any(have_consumers)
                 b_push = all(have_consumers)
                 if b_push:
@@ -175,8 +204,9 @@ def main(fname: str, playback_speed: float = 1.0, loop: bool = True, wait_for_co
                         # Irregular rate, like events and markers
                         for dat_idx in range(start_idx, stop_idx):
                             sample = streams[streamer.stream_ix]["time_series"][dat_idx]
-                            streamer.outlet.push_sample(sample,
-                                                        timestamp=timer.t0 + streamer.tvec[dat_idx])
+                            streamer.outlet.push_sample(
+                                sample, timestamp=timer.t0 + streamer.tvec[dat_idx]
+                            )
                             # print(f"Pushed sample: {sample}")
                     read_heads[streamer.name] = stop_idx
             timer.sleep()
@@ -186,14 +216,19 @@ def main(fname: str, playback_speed: float = 1.0, loop: bool = True, wait_for_co
 
 
 if __name__ == "__main__":
-    parser = argparse.ArgumentParser(description="Playback an XDF file over LSL streams.")
+    parser = argparse.ArgumentParser(
+        description="Playback an XDF file over LSL streams."
+    )
+    parser.add_argument("filename", type=str, help="Path to the XDF file")
     parser.add_argument(
-        "filename",
-        type=str,
-        help="Path to the XDF file"
+        "--playback_speed", type=float, default=1.0, help="Playback speed multiplier."
     )
-    parser.add_argument("--playback_speed", type=float, default=1.0, help="Playback speed multiplier.")
     parser.add_argument("--loop", action="store_false")
     parser.add_argument("--wait_for_consumer", action="store_true")
     args = parser.parse_args()
-    main(args.filename, playback_speed=args.playback_speed, loop=args.loop, wait_for_consumer=args.wait_for_consumer)
+    main(
+        args.filename,
+        playback_speed=args.playback_speed,
+        loop=args.loop,
+        wait_for_consumer=args.wait_for_consumer,
+    )

pyxdf/examples/print_metadata.py

@@ -3,30 +3,33 @@
 #          Chadwick Boulay
 #
 # License: BSD (2-clause)
-from os.path import abspath, join, dirname
-import logging
 import argparse
+import logging
+from os.path import abspath, dirname, join
 
 import pyxdf
 
 
 def main(fname: str):
     logging.basicConfig(level=logging.DEBUG)  # Use logging.INFO to reduce output
-    streams, fileheader = pyxdf.load_xdf(fname)
+    streams, _ = pyxdf.load_xdf(fname)
 
     print("Found {} streams:".format(len(streams)))
     for ix, stream in enumerate(streams):
         msg = "Stream {}: {} - type {} - uid {} - shape {} at {} (effective {}) Hz"
-        print(msg.format(
-            ix + 1, stream['info']['name'][0],
-            stream['info']['type'][0],
-            stream['info']['uid'][0],
-            (int(stream['info']['channel_count'][0]), len(stream['time_stamps'])),
-            stream['info']['nominal_srate'][0],
-            stream['info']['effective_srate'])
+        print(
+            msg.format(
+                ix + 1,
+                stream["info"]["name"][0],
+                stream["info"]["type"][0],
+                stream["info"]["uid"][0],
+                (int(stream["info"]["channel_count"][0]), len(stream["time_stamps"])),
+                stream["info"]["nominal_srate"][0],
+                stream["info"]["effective_srate"],
+            )
         )
-        if any(stream['time_stamps']):
-            duration = stream['time_stamps'][-1] - stream['time_stamps'][0]
+        if any(stream["time_stamps"]):
+            duration = stream["time_stamps"][-1] - stream["time_stamps"][0]
             print("\tDuration: {} s".format(duration))
     print("Done.")
 
@@ -37,7 +40,7 @@ def main(fname: str):
         "-f",
         type=str,
         help="Path to the XDF file",
-        default=abspath(join(dirname(__file__), "..", "..", "..", "xdf_sample.xdf"))
+        default=abspath(join(dirname(__file__), "..", "..", "..", "xdf_sample.xdf")),
     )
     args = parser.parse_args()
     main(args.f)

pyxdf/pyxdf.py

@@ -9,18 +9,18 @@
 
 This function is closely following the load_xdf reference implementation.
 """
+
+import gzip
 import io
-import struct
 import itertools
-import gzip
-from xml.etree.ElementTree import fromstring, ParseError
-from collections import OrderedDict, defaultdict
 import logging
+import struct
+from collections import OrderedDict, defaultdict
 from pathlib import Path
+from xml.etree.ElementTree import ParseError, fromstring
 
 import numpy as np
 
-
 __all__ = ["load_xdf"]
 
 logger = logging.getLogger(__name__)
@@ -81,7 +81,7 @@ def load_xdf(
     clock_reset_threshold_offset_seconds=1,
     clock_reset_threshold_offset_stds=10,
     winsor_threshold=0.0001,
-    verbose=None
+    verbose=None,
 ):
     """Import an XDF file.
 
@@ -210,9 +210,7 @@ def load_xdf(
     elif isinstance(select_streams, int):
         select_streams = [select_streams]
     elif all([isinstance(elem, dict) for elem in select_streams]):
-        select_streams = match_streaminfos(
-            resolve_streams(filename), select_streams
-        )
+        select_streams = match_streaminfos(resolve_streams(filename), select_streams)
         if not select_streams:  # no streams found
             raise ValueError("No matching streams found.")
     elif not all([isinstance(elem, int) for elem in select_streams]):
@@ -306,9 +304,7 @@ def load_xdf(
                 # noinspection PyBroadException
                 try:
                     nsamples, stamps, values = _read_chunk3(f, temp[StreamId])
-                    logger.debug(
-                        "  reading [%s,%s]" % (temp[StreamId].nchns, nsamples)
-                    )
+                    logger.debug("  reading [%s,%s]" % (temp[StreamId].nchns, nsamples))
                     # optionally send through the on_chunk function
                     if on_chunk is not None:
                         values, stamps, streams[StreamId] = on_chunk(
@@ -337,12 +333,8 @@ def load_xdf(
                     )
             elif tag == 4:
                 # read [ClockOffset] chunk
-                temp[StreamId].clock_times.append(
-                    struct.unpack("<d", f.read(8))[0]
-                )
-                temp[StreamId].clock_values.append(
-                    struct.unpack("<d", f.read(8))[0]
-                )
+                temp[StreamId].clock_times.append(struct.unpack("<d", f.read(8))[0])
+                temp[StreamId].clock_values.append(struct.unpack("<d", f.read(8))[0])
             else:
                 # skip other chunk types (Boundary, ...)
                 f.read(chunklen - 2)
@@ -509,7 +501,7 @@ def _xml2dict(t):
 
 def _scan_forward(f):
     """Scan forward through file object until after the next boundary chunk."""
-    blocklen = 2 ** 20
+    blocklen = 2**20
     signature = bytes(
         [
             0x43,
@@ -577,28 +569,18 @@ def _clock_sync(
 
                 # points where a glitch in the timing of successive clock
                 # measurements happened
-                mad = (
-                    np.median(np.abs(time_diff - median_ival))
-                    + np.finfo(float).eps
-                )
+                mad = np.median(np.abs(time_diff - median_ival)) + np.finfo(float).eps
                 cond1 = time_diff < 0
                 cond2 = (time_diff - median_ival) / mad > reset_threshold_stds
                 cond3 = time_diff - median_ival > reset_threshold_seconds
                 time_glitch = cond1 | (cond2 & cond3)
 
                 # Points where a glitch in successive clock value estimates
                 # happened
-                mad = (
-                    np.median(np.abs(value_diff - median_slope))
-                    + np.finfo(float).eps
-                )
+                mad = np.median(np.abs(value_diff - median_slope)) + np.finfo(float).eps
                 cond1 = value_diff < 0
-                cond2 = (
-                    value_diff - median_slope
-                ) / mad > reset_threshold_offset_stds
-                cond3 = (
-                    value_diff - median_slope > reset_threshold_offset_seconds
-                )
+                cond2 = (value_diff - median_slope) / mad > reset_threshold_offset_stds
+                cond3 = value_diff - median_slope > reset_threshold_offset_seconds
                 value_glitch = cond1 | (cond2 & cond3)
                 resets_at = time_glitch & value_glitch
 
@@ -607,9 +589,7 @@ def _clock_sync(
                     ranges = [(0, len(clock_times) - 1)]
                 else:
                     indices = np.where(resets_at)[0]
-                    indices = np.hstack(
-                        (0, indices, indices + 1, len(resets_at) - 1)
-                    )
+                    indices = np.hstack((0, indices, indices + 1, len(resets_at) - 1))
                     ranges = np.reshape(indices, (2, -1)).T
 
             # Otherwise we just assume that there are no clock resets
@@ -624,8 +604,7 @@ def _clock_sync(
                     X = np.column_stack(
                         [
                             np.ones((stop - start,)),
-                            np.array(clock_times[start:stop])
-                            / winsor_threshold,
+                            np.array(clock_times[start:stop]) / winsor_threshold,
                         ]
                     )
                     y = np.array(clock_values[start:stop]) / winsor_threshold
@@ -638,9 +617,7 @@ def _clock_sync(
 
             # Apply the correction to all time stamps
             if len(ranges) == 1:
-                stream.time_stamps += coef[0][0] + (
-                    coef[0][1] * stream.time_stamps
-                )
+                stream.time_stamps += coef[0][0] + (coef[0][1] * stream.time_stamps)
             else:
                 for coef_i, range_i in zip(coef, ranges):
                     r = slice(range_i[0], range_i[1])