2.0.1

.github/pull_request_template.md

@@ -1,10 +1,6 @@
 # Overview
 
-Define what you did...
-
-## Ticket
-
-Link a pivotal ticket here
+Define what you did... why is this change required? What problem does it solve?
 
 ## Contributions
 

.github/workflows/main.yml

@@ -115,9 +115,9 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         brew update
+        brew uninstall cmake
         sh scripts/shell/m2chip_install.sh
         brew install labstreaminglayer/tap/lsl
-        pip install psychopy --no-deps
         make install
     - name: install dependencies
       run: |
@@ -136,7 +136,4 @@ jobs:
     - name: build
       run: |
         make build
-    - name: codacy
-      run: |
-        export CODACY_PROJECT_TOKEN=${{ secrets.CODACY_PROJECT_TOKEN }}
-        bash <(curl -Ls https://coverage.codacy.com/get.sh) report -r "cobertura.xml"
+

.github/workflows/publish_to_pypi.yml

@@ -83,17 +83,16 @@ jobs:
       env:
         GITHUB_TOKEN: ${{ github.token }}
       run: >-
-        gh release create
-        "$GITHUB_REF_NAME"
-        --repo "$GITHUB_REPOSITORY"
+        VERSION=$(python -c "import toml; print(toml.load('pyproject.toml')['project']['version'])")
+        gh release create \
+        "v${VERSION}" \
+        --repo "$GITHUB_REPOSITORY" \
         --notes ""
     - name: Upload artifact signatures to GitHub Release
       env:
         GITHUB_TOKEN: ${{ github.token }}
-      # Upload to GitHub Release using the `gh` CLI.
-      # `dist/` contains the built packages, and the
-      # sigstore-produced signatures and certificates.
-      run: >-
-        gh release upload
-        "$GITHUB_REF_NAME" dist/**
+      run: |
+        VERSION=$(python -c "import toml; print(toml.load('pyproject.toml')['project']['version'])")
+        gh release upload \
+        "v${VERSION}" dist/** \
         --repo "$GITHUB_REPOSITORY"

CHANGELOG.md

@@ -1,3 +1,9 @@
+# 2.0.1
+
+- Update PsychoPy to 2025.1.1
+- Update MacOS builds to remove cmake before lsl install
+- Fix EEG evidence bug in copy phrase task
+
 # 2.0.0
 
 The next major BciPy release is here! All features included from release canidates rc1-rc4 and contributions described below.

bcipy/core/symbols.py

@@ -32,12 +32,12 @@ def alphabet(parameters: Optional[Any] = None, include_path: bool = True,
         stimulus_array: List[str] = []
         for stimulus_filename in sorted(os.listdir(path)):
             # PLUS.png is reserved for the fixation symbol
-            if stimulus_filename.endswith(
-                    '.png') and not stimulus_filename.endswith('PLUS.png'):
+            root, ext = os.path.splitext(stimulus_filename)
+            if ext in [".png", ".bmp", ".jpg"] and not root.endswith("PLUS"):
                 if include_path:
                     img = os.path.join(path, stimulus_filename)
                 else:
-                    img = os.path.splitext(stimulus_filename)[0]
+                    img = root
                 stimulus_array.append(img)
         return stimulus_array
 

bcipy/core/tests/resources/images/text.txt

@@ -0,0 +1 @@
+Text file for testing only images are collected from the folder.

bcipy/core/tests/test_symbols.py

@@ -1,7 +1,7 @@
 import unittest
 
 from bcipy.core.symbols import alphabet
-
+from typing import Dict
 
 class TestAlphabet(unittest.TestCase):
     def test_alphabet_text(self):
@@ -17,15 +17,26 @@ def test_alphabet_text(self):
             '<', '_'
         ])
 
-    def test_alphabet_images(self):
-        parameters = {}
+    def test_alphabet_images_with_path(self):
+        path = 'bcipy/core/tests/resources/images/'
+        parameters: Dict[str, bool | str] = {}
         parameters['is_txt_stim'] = False
-        parameters['path_to_presentation_images'] = ('bcipy/static/images/'
-                                                     'rsvp/')
+        parameters['path_to_presentation_images'] = path
 
         alp = alphabet(parameters)
 
-        self.assertNotEqual(alp, [
-            'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M',
-            'N', 'O', 'P', 'R', 'S', 'T', 'U', 'V', 'Y', 'Z', '<', '_'
+        self.assertEqual(alp, [
+            path + 'a_1x1.bmp',
+            path + 'b_1x1.jpg',
+            path + 'c_1x1.png'
         ])
+
+    def test_alphabet_images_without_path(self):
+        path = 'bcipy/core/tests/resources/images/'
+        parameters: Dict[str, bool | str] = {}
+        parameters['is_txt_stim'] = False
+        parameters['path_to_presentation_images'] = path
+
+        alp = alphabet(parameters, include_path=False)
+
+        self.assertEqual(alp, ['a_1x1', 'b_1x1', 'c_1x1'])

bcipy/display/paradigm/rsvp/display.py

@@ -319,7 +319,7 @@ def _generate_inquiry(self) -> List[Dict[str, Any]]:
             this_stimuli_size = (self.size_list_sti[idx] if self.size_list_sti
                                  else self.stimuli_height)
 
-            if stim.endswith('.png'):
+            if any([stim.endswith(ext) for ext in [".png", ".bmp", ".jpg"]]):
                 current_stim['sti'] = self._create_stimulus(
                     mode='image',
                     height=this_stimuli_size,

bcipy/gui/BCInterface.py

@@ -172,8 +172,8 @@ def _build_action_buttons(self) -> None:
             (self.ui_config.btn_width * 2) + 20
         self.add_button(
             message='Train',
-            position=(btn_auc_x, 450),
-            size=(self.ui_config.btn_width, self.ui_config.btn_height),
+            position=[btn_auc_x, 450],
+            size=[self.ui_config.btn_width, self.ui_config.btn_height],
             background_color='LightSeaGreen',
             text_color='black',
             font_family=self.ui_config.font,
@@ -182,7 +182,7 @@ def _build_action_buttons(self) -> None:
     def _build_start_button(self) -> None:
         """Build the Start Session button."""
         btn_start_width = self.ui_config.btn_width * 2 + 10
-        btn_start_x = self.width - (self.ui_config.padding + btn_start_width)
+        btn_start_x = self._width - (self.ui_config.padding + btn_start_width)
         self.add_button(
             message='Start Session',
             position=[btn_start_x, 440],
@@ -196,7 +196,7 @@ def _build_create_experiment_button(self) -> None:
         """Build the Create Experiment button."""
         self.add_button(
             message='+',
-            position=[self.width - self.ui_config.padding - 200, 260],
+            position=[self._width - self.ui_config.padding - 200, 260],
             size=[35, self.ui_config.btn_height - 10],
             background_color='green',
             action=self.create_experiment,
@@ -301,7 +301,7 @@ def build_images(self) -> None:
         # NEU logo
         self.add_image(
             path=f'{STATIC_IMAGES_PATH}/gui/neu.png',
-            position=[self.width - self.ui_config.padding - 110, 0],
+            position=[self._width - self.ui_config.padding - 110, 0],
             size=100)
 
     def build_assets(self) -> None:
@@ -517,7 +517,7 @@ def load_experiments(self) -> List[str]:
         Returns:
             List[str]: List of experiment names.
         """
-        return load_experiments().keys()
+        return list(load_experiments().keys())
 
     def start_experiment(self) -> None:
         """Start an experiment session."""

bcipy/parameters/parameters.json

@@ -267,7 +267,7 @@
     "value": "bcipy/static/images/rsvp/",
     "section": "bci_config",
     "name": "Image Stimulus Folder",
-    "helpTip": "Specifies the location of image files to be used as stimuli (Text Stimuli On/Off must be set to ‘false’). This must be a directory ending with /.",
+    "helpTip": "Specifies the location of image files to be used as stimuli (Text Stimuli On/Off must be set to ‘false’). This must be a directory ending with /. Image files must have extension .bmp, .jpg, or .png. Files ending in PLUS.bmp, PLUS.jpg, or PLUS.png, are ignored as they are assumed to be fixation images.",
     "recommended": "",
     "editable": false,
     "type": "directorypath"

bcipy/task/control/evidence.py

@@ -61,6 +61,7 @@ def __init__(
         self.symbol_set = symbol_set
         self.signal_model = signal_model
         self.device_spec = device_spec
+        self.parameters = parameters
 
     @property
     def consumes(self) -> ContentType:
@@ -80,7 +81,7 @@ def produces(self) -> EvidenceType:
         """
         raise NotImplementedError()
 
-    def evaluate(self, **kwargs: Any) -> np.ndarray:
+    def evaluate(self, *args: Any, **kwargs: Any) -> np.ndarray:
         """Evaluate the evidence from raw data.
 
         Args:
@@ -167,7 +168,8 @@ def evaluate(
             times: List[float],
             target_info: List[str],
             window_length: float,
-            *args: Any) -> np.ndarray:
+            *args: Any,
+            **kwargs: Any) -> np.ndarray:
         """Evaluate EEG evidence.
 
         Args:
@@ -270,10 +272,9 @@ def evaluate(
             raw_data: np.ndarray,
             symbols: List[str],
             times: List[float],
-            target_info: List[str],
-            window_length: float,
             flash_time: float,
-            stim_length: float) -> np.ndarray:
+            *args: Any,
+            **kwargs: Any) -> np.ndarray:
         """Evaluate gaze evidence.
 
         Args:
@@ -382,7 +383,7 @@ def preprocess(
     # pylint: disable=arguments-differ
     def evaluate(self, raw_data: np.ndarray, symbols: List[str],
                  times: List[float], target_info: List[str],
-                 window_length: float) -> np.ndarray:
+                 window_length: float, *args: Any, **kwargs: Any) -> np.ndarray:
         """Evaluate the evidence.
 
         Parameters

bcipy/task/paradigm/rsvp/copy_phrase.py

@@ -648,7 +648,7 @@ def evaluate_evidence(self) -> Decision:
         return Decision(decision_made, selection, spelled_text, new_sti)
 
     def add_evidence(
-        self, stim_times: List[List], proceed: bool = True
+        self, stim_times: List[Tuple], proceed: bool = True
     ) -> List[EvidenceType]:
         """Add all evidence used to make a decision.
 

pyproject.toml

@@ -4,7 +4,7 @@ requires = ["setuptools>=61.0", "wheel>=0.37.1"]
 
 [project]
 name = "bcipy"
-version = "2.0.0"
+version = "2.0.1"
 authors = [
     {name="CAMBI", email="[email protected]"},
 ]
@@ -34,7 +34,7 @@ dependencies = [
     "pybv==0.7.5",
     "pyo==1.0.5",
     "pyglet<=1.5.27,>=1.4",
-    "PsychoPy==2024.2.1",
+    "PsychoPy==2025.1.1",
     "openpyxl==3.1.2",
     "numpy==1.24.4",
     "sounddevice==0.4.4",