Improve CIs, example and code coverage

.github/actions/get-testing-dataset/action.yaml

@@ -0,0 +1,44 @@
+name: "Get MNE-LSL testing dataset"
+description: "A composite action to get MNE-LSL testing dataset from cache or remote."
+inputs:
+  sample:
+    description: "If True, retrieve the sample dataset."
+    required: false
+    default: "false"
+  testing:
+    description: "If True, retrieve the testing dataset."
+    required: false
+    default: "true"
+
+runs:
+  using: "composite"
+  steps:
+    - name: Get dataset version file
+      shell: bash
+      run: |
+          curl https://raw.githubusercontent.com/mscheltienne/mne-lsl-datasets/main/version.txt -o mne_lsl_dataset_version.txt
+    - name: Cache testing dataset
+      if: ${{ inputs.testing == 'true' }}
+      id: cache_testing
+      uses: actions/cache@v4
+      with:
+        key: mne-lsl-testing-${{ runner.os }}-${{ hashFiles('mne_lsl_dataset_version.txt') }}
+        path: ~/mne_data/MNE-LSL-data/testing
+    - name: Download testing dataset
+      if: ${{ inputs.testing == 'true' && steps.cache_testing.outputs.cache-hit != 'true' }}
+      shell: bash
+      run: python -c "import mne_lsl; mne_lsl.datasets.testing.data_path()"
+    - name: Cache sample dataset
+      if: ${{ inputs.sample == 'true' }}
+      id: cache_sample
+      uses: actions/cache@v4
+      with:
+        key: mne-lsl-sample-${{ runner.os }}-${{ hashFiles('mne_lsl_dataset_version.txt') }}
+        path: ~/mne_data/MNE-LSL-data/sample
+    - name: Download sample dataset
+      if: ${{ inputs.sample == 'true' && steps.cache_sample.outputs.cache-hit != 'true' }}
+      shell: bash
+      run: python -c "import mne_lsl; mne_lsl.datasets.sample.data_path()"
+    - name: Remove dataset version file
+      shell: bash
+      run: rm mne_lsl_dataset_version.txt

.github/actions/install-system-dependencies/action.yaml

@@ -0,0 +1,37 @@
+name: "Install system dependencies"
+description: "A composite action to install liblsl and system dependencies on different operating systems."
+
+runs:
+  using: "composite"
+  steps:
+    - name: Install linux dependencies
+      if: ${{ runner.os == 'Linux' }}
+      shell: bash
+      run: |
+        sudo apt update
+        sudo apt install -y binutils libpugixml-dev qtbase5-dev qt5-qmake
+    - name: Install liblsl (linux)
+      if: ${{ runner.os == 'Linux' }}
+      shell: bash
+      run: |
+        curl -L https://github.com/sccn/liblsl/releases/download/v1.16.2/liblsl-1.16.2-jammy_amd64.deb -o liblsl-1.16.2-jammy_amd64.deb
+        sudo apt install -y ./liblsl-1.16.2-jammy_amd64.deb
+        rm liblsl-1.16.2-jammy_amd64.deb
+    - name: Install liblsl (macOS)
+      if: ${{ runner.os == 'macOS' }}
+      shell: bash
+      run: |
+        curl -L https://github.com/sccn/liblsl/releases/download/v1.16.0/liblsl-1.16.0-OSX_arm64.tar.bz2 -o liblsl-1.16.0-OSX_arm64.tar.bz2
+        tar -xf liblsl-1.16.0-OSX_arm64.tar.bz2
+        mv lib/liblsl.1.16.0.dylib .
+        echo "MNE_LSL_LIB=$PWD/liblsl.1.16.0.dylib" >> $GITHUB_ENV
+        rm -R lib include bin
+        rm liblsl-1.16.0-OSX_arm64.tar.bz2
+    - name: Install liblsl (windows)
+      if: ${{ runner.os == 'Windows' }}
+      shell: bash
+      run: |
+        curl -L https://github.com/sccn/liblsl/releases/download/v1.16.2/liblsl-1.16.2-Win_amd64.zip -o liblsl-1.16.2-Win_amd64.zip
+        7z x -oliblsl liblsl-1.16.2-Win_amd64.zip
+        echo "MNE_LSL_LIB=$PWD/liblsl/bin/lsl.dll" >> $GITHUB_ENV
+        rm liblsl-1.16.2-Win_amd64.zip

.github/workflows/doc.yaml

@@ -22,25 +22,23 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: 3.11
-      - name: Install linux dependencies
-        run: |
-          curl -L https://github.com/sccn/liblsl/releases/download/v1.16.2/liblsl-1.16.2-jammy_amd64.deb -o liblsl-1.16.2-jammy_amd64.deb
-          sudo apt update
-          sudo apt install -y libpugixml-dev qtbase5-dev qt5-qmake optipng
-          sudo apt install -y ./liblsl-1.16.2-jammy_amd64.deb
-          rm liblsl-1.16.2-jammy_amd64.deb
+      - name: Install system dependencies
+        uses: ./.github/actions/install-system-dependencies
+      - name: Install optipng (for sphinx-gallery)
+        run: sudo apt install optipng
       - name: Install package
         run: |
           python -m pip install --progress-bar off --upgrade pip setuptools
           python -m pip install --progress-bar off .[doc]
       - name: Display system information
         run: mne_lsl-sys_info --developer
-      - name: Build doc
-        uses: nick-fields/retry@v3
+      - name: Get dataset
+        uses: ./.github/actions/get-testing-dataset
         with:
-          timeout_minutes: 10
-          max_attempts: 3
-          command: make -C doc html
+          sample: "true"
+          testing: "false"
+      - name: Build doc
+        run: make -C doc html
       - name: Prune sphinx environment
         run: rm -R ./doc/_build/html/.doctrees
       - name: Upload documentation

.github/workflows/publish.yaml

@@ -15,14 +15,9 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: 3.11
-      - name: Install linux dependencies
-        run: |
-          curl -L https://github.com/sccn/liblsl/releases/download/v1.16.2/liblsl-1.16.2-jammy_amd64.deb -o liblsl-1.16.2-jammy_amd64.deb
-          sudo apt update
-          sudo apt install -y libpugixml-dev qtbase5-dev qt5-qmake optipng
-          sudo apt install -y ./liblsl-1.16.2-jammy_amd64.deb
-          rm liblsl-1.16.2-jammy_amd64.deb
-      - name: Install dependencies
+      - name: Install system dependencies
+        uses: ./.github/actions/install-system-dependencies
+      - name: Install package
         run: |
           python -m pip install --progress-bar off --upgrade pip setuptools
           python -m pip install --progress-bar off -e .[build,stubs]

.github/workflows/pytest.yaml

@@ -28,36 +28,16 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Install liblsl (linux)
-        if: ${{ matrix.os == 'ubuntu' }}
-        run: |
-          curl -L https://github.com/sccn/liblsl/releases/download/v1.16.2/liblsl-1.16.2-jammy_amd64.deb -o liblsl-1.16.2-jammy_amd64.deb
-          sudo apt update
-          sudo apt install -y binutils libpugixml-dev qtbase5-dev qt5-qmake
-          sudo apt install -y ./liblsl-1.16.2-jammy_amd64.deb
-          rm liblsl-1.16.2-jammy_amd64.deb
-      - name: Install liblsl (macOS)
-        if: ${{ matrix.os == 'macos' }}
-        run: |
-          curl -L https://github.com/sccn/liblsl/releases/download/v1.16.0/liblsl-1.16.0-OSX_arm64.tar.bz2 -o liblsl-1.16.0-OSX_arm64.tar.bz2
-          tar -xf liblsl-1.16.0-OSX_arm64.tar.bz2
-          mv lib/liblsl.1.16.0.dylib .
-          echo "MNE_LSL_LIB=$PWD/liblsl.1.16.0.dylib" >> $GITHUB_ENV
-          rm -R lib include bin
-          rm liblsl-1.16.0-OSX_arm64.tar.bz2
-      - name: Install liblsl (windows)
-        if: ${{ matrix.os == 'windows' }}
-        run: |
-          curl -L https://github.com/sccn/liblsl/releases/download/v1.16.2/liblsl-1.16.2-Win_amd64.zip -o liblsl-1.16.2-Win_amd64.zip
-          7z x -oliblsl liblsl-1.16.2-Win_amd64.zip
-          echo "MNE_LSL_LIB=$PWD/liblsl/bin/lsl.dll" >> $GITHUB_ENV
-          rm liblsl-1.16.2-Win_amd64.zip
-      - name: Install dependencies
+      - name: Install system dependencies
+        uses: ./.github/actions/install-system-dependencies
+      - name: Install package
         run: |
           python -m pip install --progress-bar off --upgrade pip setuptools
           python -m pip install --progress-bar off .[test]
       - name: Display system information
         run: mne_lsl-sys_info --developer
+      - name: Get testing dataset
+        uses: ./.github/actions/get-testing-dataset
       - name: Run pytest
         run: pytest mne_lsl --cov=mne_lsl --cov-report=xml --cov-config=pyproject.toml -s
         env:
@@ -90,13 +70,9 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Install liblsl & linux dependencies
-        run: |
-          curl -L https://github.com/sccn/liblsl/releases/download/v1.16.2/liblsl-1.16.2-jammy_amd64.deb -o liblsl-1.16.2-jammy_amd64.deb
-          sudo apt update
-          sudo apt install -y binutils libpugixml-dev qtbase5-dev qt5-qmake
-          sudo apt install -y ./liblsl-1.16.2-jammy_amd64.deb
-      - name: Install dependencies
+      - name: Install system dependencies
+        uses: ./.github/actions/install-system-dependencies
+      - name: Install package
         run: |
           python -m pip install --progress-bar off --upgrade pip setuptools
           python -m pip install --progress-bar off .[test]
@@ -106,6 +82,8 @@ jobs:
           python -m pip install --progress-bar off --upgrade --pre --only-binary :all: -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple --timeout=180 numpy scipy
       - name: Display system information
         run: mne_lsl-sys_info --developer
+      - name: Get testing dataset
+        uses: ./.github/actions/get-testing-dataset
       - name: Run pytest
         run: pytest mne_lsl --cov=mne_lsl --cov-report=xml --cov-config=pyproject.toml -s
         env:
@@ -139,21 +117,18 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Install liblsl (linux)
-        run: |
-          curl -L https://github.com/sccn/liblsl/releases/download/v1.16.2/liblsl-1.16.2-jammy_amd64.deb -o liblsl-1.16.2-jammy_amd64.deb
-          sudo apt update
-          sudo apt install -y binutils libpugixml-dev qtbase5-dev qt5-qmake
-          sudo apt install -y ./liblsl-1.16.2-jammy_amd64.deb
-          rm liblsl-1.16.2-jammy_amd64.deb
-      - name: Install dependencies
+      - name: Install system dependencies
+        uses: ./.github/actions/install-system-dependencies
+      - name: Install package
         run: |
           python -m pip install --progress-bar off --upgrade pip setuptools
           python -m pip install --progress-bar off .[test]
           python -m pip uninstall mne -y
           python -m pip install --progress-bar off mne==${{ matrix.mne-version }}
       - name: Display system information
         run: mne_lsl-sys_info --developer
+      - name: Get testing dataset
+        uses: ./.github/actions/get-testing-dataset
       - name: Run pytest
         run: pytest mne_lsl --cov=mne_lsl --cov-report=xml --cov-config=pyproject.toml -s
         env:

.github/workflows/stubs.yaml

@@ -22,13 +22,8 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: 3.11
-      - name: Install linux dependencies
-        run: |
-          curl -L https://github.com/sccn/liblsl/releases/download/v1.16.2/liblsl-1.16.2-jammy_amd64.deb -o liblsl-1.16.2-jammy_amd64.deb
-          sudo apt update
-          sudo apt install -y libpugixml-dev qtbase5-dev qt5-qmake
-          sudo apt install -y ./liblsl-1.16.2-jammy_amd64.deb
-          rm liblsl-1.16.2-jammy_amd64.deb
+      - name: Install system dependencies
+        uses: ./.github/actions/install-system-dependencies
       - name: Install package
         run: |
           python -m pip install --progress-bar off --upgrade pip setuptools

examples/00_peak_detection.py → examples/10_peak_detection.py

@@ -288,6 +288,7 @@ def __init__(
         self._stream.notch_filter(100, picks=ch_name)
         sleep(bufsize)  # prefill an entire buffer
         # peak detection settings
+        self._last_acq_time = None
         self._last_peak = None
         self._peak_candidates = None
         self._peak_candidates_count = None
@@ -301,6 +302,11 @@ def detect_peaks(self) -> NDArray[np.float64]:
             The timestamps of all detected peaks.
         """
         data, ts = self._stream.get_data()  # we have a single channel in the stream
+        if self._last_acq_time is None:
+            self._last_acq_time = ts[-1]
+        elif self._last_acq_time == ts[-1]:
+            self._last_acq_time = ts[-1]
+            return np.array([])  # nothing new to do
         data = data.squeeze()
         peaks, _ = find_peaks(
             data,

mne_lsl/datasets/testing.py

@@ -44,7 +44,7 @@ def data_path() -> Path:
     path = (
         Path(get_config("MNE_DATA", Path.home())).expanduser()
         / "mne_data"
-        / "MNE-LSL"
+        / "MNE-LSL-data"
         / "testing"
     )
     base_url = "https://github.com/mscheltienne/mne-lsl-datasets/raw/main/testing"

mne_lsl/player/player_lsl.py

@@ -279,7 +279,7 @@ def _stream(self) -> None:
             else:
                 self._outlet.push_chunk(data, timestamp=self._target_timestamp)
             self._stream_annotations(start, stop, start_timestamp)
-        except Exception as exc:
+        except Exception as exc:  # pragma: no cover
             logger.error("%s: Stopping due to exception: %s", self._name, exc)
             self._del_outlets()
             self._reset_variables()
@@ -296,8 +296,8 @@ def _stream(self) -> None:
             sleep(delay)
             try:
                 self._executor.submit(self._stream)
-            except RuntimeError:
-                assert self._executor._shutdown  # pragma: no cover
+            except RuntimeError:  # pragma: no cover
+                pass  # shutdown
 
     def _stream_annotations(
         self, start: int, stop: int, start_timestamp: float

mne_lsl/player/tests/test_player_lsl.py

@@ -114,6 +114,7 @@ def test_player_context_manager_raw_annotations(raw_annotations):
     with Player(
         raw_annotations, chunk_size=200, name=name, annotations=False
     ) as player:
+        assert player.running
         streams = resolve_streams(timeout=2)
         assert len(streams) == 1
         assert streams[0].name == name
@@ -122,6 +123,7 @@ def test_player_context_manager_raw_annotations(raw_annotations):
     assert len(streams) == 0
 
     with Player(raw_annotations, chunk_size=200, name=name) as player:
+        assert player.running
         streams = resolve_streams(timeout=2)
         assert len(streams) == 2
         assert any(stream.name == name for stream in streams)
@@ -336,6 +338,7 @@ def test_player_annotations(raw_annotations, close_io):
     name = "Player-test_player_annotations"
     annotations = sorted(set(raw_annotations.annotations.description))
     player = Player(raw_annotations, chunk_size=200, name=name)
+    assert f"Player: {name}" in repr(player)
     assert player.name == name
     assert player.fname == Path(raw_annotations.filenames[0])
     streams = resolve_streams(timeout=0.1)
@@ -410,7 +413,10 @@ def test_player_n_repeat(raw):
     player = Player(
         raw, chunk_size=200, n_repeat=4, name="Player-test_player_n_repeat-2"
     )
+    assert player.n_repeat == 4
     player.start()
+    assert player.n_repeat == 4
+    assert player.running
     time.sleep((raw.times.size / raw.info["sfreq"]) * 1.8)
     assert player._executor is not None
     streams = resolve_streams(timeout=2)

mne_lsl/stream/_base.py

@@ -567,7 +567,7 @@ def get_data(
                     "The Stream is not connected. Please connect to the stream before "
                     "retrieving data from the buffer."
                 )
-            else:
+            else:  # pragma: no cover
                 logger.error(
                     "Something went wrong while retrieving data from a connected "
                     "stream. Please open an issue on GitHub and provide the error "

mne_lsl/stream/stream_lsl.py

@@ -230,8 +230,8 @@ def _acquire(self) -> None:
                 sleep(self._acquisition_delay)
                 try:
                     self._executor.submit(self._acquire)
-                except RuntimeError:
-                    assert self._executor._shutdown  # pragma: no cover
+                except RuntimeError:  # pragma: no cover
+                    pass  # shutdown
                 return  # interrupt early
 
             # process acquisition window
@@ -249,8 +249,8 @@ def _acquire(self) -> None:
                 sleep(self._acquisition_delay)
                 try:
                     self._executor.submit(self._acquire)
-                except RuntimeError:
-                    assert self._executor._shutdown  # pragma: no cover
+                except RuntimeError:  # pragma: no cover
+                    pass  # shutdown
                 return  # interrupt early
             if len(self._added_channels) != 0:
                 refs = np.zeros(
@@ -296,7 +296,7 @@ def _acquire(self) -> None:
                     "argument or consider retrieving new samples more often with "
                     "Stream.get_data()."
                 )
-        except Exception as error:
+        except Exception as error:  # pragma: no cover
             logger.exception(error)
             self._reset_variables()  # disconnects from the stream
             if os.getenv("MNE_LSL_RAISE_STREAM_ERRORS", "false").lower() == "true":
@@ -305,8 +305,8 @@ def _acquire(self) -> None:
             try:
                 sleep(self._acquisition_delay)
                 self._executor.submit(self._acquire)
-            except RuntimeError:
-                assert self._executor._shutdown  # pragma: no cover
+            except RuntimeError:  # pragma: no cover
+                pass  # shutdown
 
     def _reset_variables(self) -> None:
         """Reset variables define after connection."""