2.0.0rc4 release

.coveragerc

@@ -2,15 +2,22 @@
 [run]
 omit =
         *__init__*
+        *__main__*
         */usr/local/lib*
         *tests*
         *test*
         *demo*
-        *gui/*
+        *exceptions.py
+        */gui/experiments/*
+        */gui/viewer/*
+        */gui/BCInterface.py
 
 [report]
 exclude_lines =
     pragma: no cover
     def __repr__
+    def __str__
     raise NotImplementedError
-    if __name__ == .__main__.:
+    @abstract
+    if __name__ == .__main__.:
+    logging.getLogger(__name__)

.github/workflows/main.yml

@@ -18,15 +18,15 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.8, 3.9]
+        python-version: [3.8, 3.9, 3.10.6]
 
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
+    - name: Update OS, pip & install custom dependencies
       run: |
         sudo apt-get update
         sudo apt-get install libgtk-3-dev
@@ -37,13 +37,9 @@ jobs:
         sudo apt-get install xvfb
         python -m pip install --upgrade pip
         pip install attrdict3
-        pip install -r dev_requirements.txt
-        pip install -e .
-        pip install kenlm==0.1 --global-option="--max_order=12"
-    - name: Lint with flake8
+    - name: Install dependencies
       run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 bcipy
+        make dev-install
     - name: Unit test
       if: always()
       run: |
@@ -59,66 +55,79 @@ jobs:
         else 
           echo "Ubuntu test failure"
         fi
+    - name: type-check
+      run: |
+        make type
+    - name: lint
+      run: |
+        make lint
 
   build-windows:
 
     runs-on: windows-latest
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.8, 3.9]
+        python-version: [3.8, 3.9, 3.10.6]
 
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Install dependencies for python3.9
-      if: matrix.python-version == 3.9
+    - name: update pip & install custom dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install ./.bcipy/downloads/pyWinhook-1.6.2-cp39-cp39-win_amd64.whl 
-    - name: Install dependencies
+    - name: install manually downloaded pyWinhook wheel for Python 3.9
+      if: matrix.python-version == 3.9
       run: |
-        python -m pip install --upgrade pip
-        pip install -r dev_requirements.txt
-        pip install -e .
-        pip install kenlm==0.1 --global-option="--max_order=12"
-    - name: Lint with flake8
+        pip install ./.bcipy/downloads/pyWinhook-1.6.2-cp39-cp39-win_amd64.whl
+    - name: install dependencies
       run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 bcipy
-    - name: Unit test
+        make dev-install
+    - name: unittest
       if: always()
       run: |
-        coverage run --branch --source=bcipy -m pytest --mpl -k "not slow"
+        make coverage-report
+    - name: type-check
+      run: |
+        make type
+    - name: lint
+      run: |
+        make lint
 
   build-macos:
 
     runs-on: macos-latest
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.8, 3.9]
+        python-version: [3.8, 3.9, 3.10.6]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
+    - name: update pip & install custom dependencies
       run: |
+        sh scripts/shell/m2chip_install.sh
+        brew install labstreaminglayer/tap/lsl
         python -m pip install --upgrade pip
-        pip install -r dev_requirements.txt
-        pip install -e .
-        pip install kenlm==0.1 --global-option="--max_order=12"
-    - name: Lint with flake8
+    - name: install dependencies
       run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 bcipy
-    - name: Unit test
+        make dev-install
+    - name: unittest
       if: always()
       run: |
-        coverage run --branch --source=bcipy -m pytest --mpl -k "not slow"
+        make coverage-report
+    - name: type-check
+      run: |
+        make type
+    - name: lint
+      run: |
+        make lint
+
+

.gitignore

@@ -1,33 +1,40 @@
+# OS and Package Files
 *.pyc
 *~
 .DS_Store
 .cache/
 .vscode/
 .tm_properties
 .mypy_cache/
-data/
+mypy-html.css
+.coverage
+index.html
+htmlcov/
+html/
+
 # Virtualenv
 venv/
 venv*/
 __pycache__/
 .cache/
 
 # BciPy files and directories
-calibration.csv
-rawdata.csv
+*.csv
+*.pdf
 buffer.db
 lmwrap.log
 env.txt
 .idea
-.coverage
-htmlcov/
 bcipy.egg-info/
+data/
 build/
 dist/
-
 bcipy/parameters/parameters_*
 bcipy_cache
-
 bcipy/language/lms/lm_dec19_char_large_12gram.*
 bcipy/language/lms/out_*
 bcipy/language/out/
+
+
+bcipy/simulator/tests/resource/
+!bcipy/simulator/data

CHANGELOG.md

@@ -1,9 +1,79 @@
-# 2.0.1-rc.3
+# 2.0.0-rc.4
+
+Our final release candidate before the official 2.0 release!
 
 ## Contributions
 
-- Bug Fixes
-    - Fix for missing inits and static assets #284 catch sessions with no data #284 move experiment and field assets to parameters location #284
+- Multimodal Acquisition and Querying
+    - Support for multiple devices in online querying #286
+    - Support for trigger handling relative to a given device #293
+    - Support multiple device static offests #331
+    - Support for Device Status (passive or active) #310
+- Session Orchestrator #339
+    - New task protocol for orchestrating tasks in a session. This refactors several Task and Cli functionality #339, #343
+    - Parameter guardrails #340
+    - Allow multiple phrases in a single protocol to be defined in a phrase.json and randomized #352
+- BciPy Client Additions #346
+  - Other commands added for offline analysis, visualization and simulation.
+- Artifact Module #336
+- Simulator #350
+- Task
+  - Calibration Task Refactor: pulls out common elements from RSVP and Matrix calibration tasks #330
+  - Registry Refactor #332
+  - Inquiry Preview
+    - Surface button error probability #347
+    - Add to Matrix #353
+    - Bugfixes/Refactor #348
+  - Add more stoppage criteria #351 (max_incorrect)
+  - Matrix 
+    - Layout Support #349
+    - Grid always on #313
+    - Output stimuli position, screen capture and monitor information after Matrix tasks #303
+    - Row/Column spacing support #298
+  - VEP Calibration #304/#296
+    - session data to VEP calibration #322
+- Model
+    - Offline analysis to support multimodal fusion. Initial release of GazeModel, GazeReshaper, and Gaze Visualization #294
+    - Updates to ensure seamless offline analysis for both EEG and Gaze data #305
+    - Offline analysis support for EEG and (multiple) gaze models. Updates to support Eye Tracker Evidence class #360
+- Language Model
+  - Add Oracle model #316
+  - Random Uniform model #311
+- Stimuli
+    - Updates to ensure stimuli are presented at the same frequency #287 
+    - Output stimuli position, screen capture and monitor information after Matrix tasks #303
+- Dynamic Selection Window
+    - Updated trial_length to trial_window to allow for greater control of window used after stimulus presentations #291
+- Report
+  - Functionality to generate a report in the form of a PDF #325
+  - Add a BciPy Calbiraiton Report Action #357
+- Offset Support
+  - Add support for determining offsets between timing verification Tasks (Ex. RSVPTimingVerificationCalibration) and RawData with a photodiode trigger column. This is useful for setting up new systems and preventing errors before an experiment begins. #327
+- Parameters
+    - Add a Range type parameter #285 Add editable fields #340 Update parameters.json to seperate relevant parameters by task
+- Housekeeping
+    - Add mypy typing to the codebase #301
+    - Change default log level to INFO to prevent too many messages in the experiment logs #288 
+    - Upgrade requirements for m1/2 chips #299/#300
+    - Fix GitHub actions build issues with macOS #324
+    - Tests Improvements
+      - Fix occasionally failing test in `test_stimuli` #326
+      - Reshaper tests #302
+    - Fix parameter save as #323
+    - Pause error #321
+    - Fix data buffer issue #308
+- GUI Refactor #337
+  - Create new `BCIUI` class for simpler more straightforward UI creation.
+  - Create dedicated external stylesheet for global styling
+  - Rewrite Experiment Registry to use new GUI code
+  - Create intertask action UI
+- Task Return Object #334
+  - Create `TaskData` dataclass to be returned from tasks
+  - updates task `execute` methods to return an instance of `TaskData`
+  - Allows for optional storage of a save path and task dictionary in `TaskData`
+-Experiment Refactor #333 #329
+  - Refactors the Experiment Field Collection GUI to be an action
+  - Allows task protocol to be defined in the orchestrator
 
 # 2.0.0-rc.3
 
@@ -17,9 +87,11 @@
     - Set channel spec information in devices.json. Removed aliases. #266 Updated default analysis channels for Wearable Sensing devices #279
     - Refactor to allow multiple devices to be configured for multimodal acquisition. #277
     - Refinements to LSL server to use the device ChannelSpec information for generating metadata. #282
+    - Updated data consumers to explicitly set a chunk size. Refinements to LSL server to simulate different chunk sizes. #292
 - Matrix
     - Matrix calibration refinements #262
     - Matrix Copy Phrase Task #261
+    - Matrix displays can be parameterized with a given number of rows and columns. #289
 - RSVP
     - RSVP Calibration pulls out inquiry preview parameters and calls the display with them if enabled
     - RSVP Display `do_inquiry` accepts a preview_calibration argument that will present the full inquiry to come if True after the prompt and before the fixation