Upgrade psychopy and add support for python3.9 (#272)

* Add cli commands for ease of testing.

Separate requirements based on platform for testing CI. Update IP with new TextBox2 properties.

* Add python3.9 support

* update workflow logic

* change logic to prevent ubuntu issue




log the system


fix syntax error


fix

* fix

* new approach

* new approach

* add attrdict

* update workflow

* Update documentation

* upgrade pandas

* update CHANGELOG

.github/workflows/main.yml

@@ -18,7 +18,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7, 3.8]
+        python-version: [3.8, 3.9]
 
     steps:
     - uses: actions/checkout@v2
@@ -36,6 +36,7 @@ jobs:
         sudo apt-get install libsndfile*
         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"
@@ -65,19 +66,23 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7, 3.8]
+        python-version: [3.8, 3.9]
 
     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
+      run: |
+        python -m pip install --upgrade pip
+        pip install ./.bcipy/downloads/pyWinhook-1.6.2-cp39-cp39-win_amd64.whl 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install -r dev_requirements.txt
-        pip install WxPython==4.1.1
         pip install -e .
         pip install kenlm==0.1 --global-option="--max_order=12"
     - name: Lint with flake8
@@ -95,7 +100,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7, 3.8]
+        python-version: [3.8, 3.9]
 
     steps:
     - uses: actions/checkout@v2
@@ -107,7 +112,6 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install -r dev_requirements.txt
-        pip install WxPython==4.1.1
         pip install -e .
         pip install kenlm==0.1 --global-option="--max_order=12"
     - name: Lint with flake8

CHANGELOG.md

@@ -19,6 +19,10 @@
     - update from `sosfilt` to `sosfiltfilt` #269
 - MNE
     - convert to mne can now handle conversion to Volts from microvolts, and no channel map #259
+- Dependencies
+    - Upgrade PsychoPy, transformers (#268) and pandas, add support for python3.9, deprecate python3.7 #272
+- BciPy client
+    - Add `-nv` (no visualizations) and `-f` (fake data) client options #272
 - Session
     - After each session run using `bci_main` an ERP visualization is generated by default using new function `visualize_session_data` #260
 - Language Model

README.md

@@ -18,23 +18,36 @@ Memmott, T., Koçanaoğulları, A., Lawhead, M., Klee, D., Dudy, S., Fried-Oken,
 
 ## Dependencies
 ---------------
-This project requires Python 3.7 or 3.8. All other dependencies defined in the requirements.txt.
+This project requires Python 3.8 or 3.9. Please see notes below for additional OS specific dependencies before installation can be completed.
 
+### Linux
+
+You will need to install the prerequisites defined in `scripts\shell\linux_requirements.sh` as well as `pip install attrdict3`.
+
+### Windows
+
+If you are using a Windows machine, you will need to install the [Microsoft Visual C++ Build Tools](https://visualstudio.microsoft.com/visual-cpp-build-tools/).
+
+*python 3.9 only!*
+You will need to install pyWinhook manually. See [here](https://www.lfd.uci.edu/~gohlke/pythonlibs/#pywinhook) for the appropriate wheel file (`pyWinhook‑1.6.2‑cp39‑cp39‑win_amd64.whl`). Then run `pip install <path_to_wheel_file>`. We also include the 64-bit wheel file in the `.bcipy/downloads/` directory.
+
+### Mac
+
+If you are using a Mac, you will need to install XCode and enable command line tools. `xcode-select --install`. 
 
 ## Installation
 ---------------
 
 #### BciPy Setup
 
-In order to run BciPy on your computer, first install **Python 3** [from here.](https://www.python.org/downloads/)
+In order to run BciPy on your computer, after following the dependencies above, you will need to install the BciPy package.
 
-To use all the goodies locally (including the GUI and demo scripts)
+To install for use locally,
 1. Git clone https://github.com/BciPy/BciPy.git
 2. Change directory in your terminal to the repo
 3. Run `pip install -e .`
-4. If using Mac, you will need to install XCode and enable command line tools. `xcode-select --install`
-5. If you're on Windows, you may need to uninstall pygame (`pip uninstall pygame`). Psychopy, for historical reasons, keeps pygame but it just spams your console logs if you only want to use pyglet (which we use in this repository!)
-6. To use the KenLMLanguageModel class, you must manually install the kenlm package. `pip install kenlm==0.1 --global-option="--max_order=12"`.
+4. To use the KenLMLanguageModel class, you must manually install the kenlm package. `pip install kenlm==0.1 --global-option="--max_order=12"`.
+
 
 If wanting the latest version from PyPi:
 1. `pip install bcipy`
@@ -48,15 +61,12 @@ make dev-install
 
 #### Usage Locally
 
-Start by running `python bcipy/gui/BCInterface.py` in your command prompt or terminal. This will run the GUI. You may also use the command `make bci-gui`. You may also invoke the experiment directly using command line tools from bcipy.
-
-Ex. `bcipy` *this will use default parameters, user, experiment and task*
-
-You can pass it attributes with flags, if desired.
-
-Ex. `bcipy --user "bci_user" --task "RSVP Calibration"`
-
-Use the help flag to see other available input options: `bcipy --help`
+Two ways to get started using BciPy for data collection:
+	1. Run `python bcipy/gui/BCInterface.py` in your command prompt or terminal from from base BciPy directory. This will execute the main BCI GUI. You may also use the command `make bci-gui`. 
+	2. Invoke the experiment directly using command line utility `bcipy`.
+		- You can pass it attributes with flags, if desired.
+				Ex. `bcipy --user "bci_user" --task "RSVP Calibration"`
+		- Use the help flag to see other available input options: `bcipy --help`
 
 ##### Example usage as a package
 

bcipy/display/paradigm/rsvp/display.py

@@ -287,21 +287,16 @@ def _generate_inquiry_preview(self) -> visual.TextBox2:
         Using the self.stimuli_inquiry list, construct a preview box to display to the user. This method
             assumes the presence of a fixation (+).
         """
-        if not self.full_screen:
-            reduce_factor = 4.85
-            wrap_width = 1.1
-        else:
-            reduce_factor = 4.75
-            wrap_width = .9
         text = ' '.join(self.stimuli_inquiry).split('+ ')[1]
 
         return self._create_stimulus(
-            self.stimuli_height / reduce_factor,
+            0.12,
             stimulus=text,
             units='height',
             stimuli_position=self.stimuli_pos,
             mode='textbox',
-            wrap_width=wrap_width)
+            align_text='left',
+            wrap_width=0.025)
 
     def _generate_inquiry(self) -> list:
         """Generate inquiry.
@@ -425,7 +420,7 @@ def _create_stimulus(
             border=False):
         """Create Stimulus.
 
-        Returns a TextStim or ImageStim object.
+        Returns a TextStim, ImageStim or TextBox object.
         """
         if not stimuli_position:
             stimuli_position = self.stimuli_pos
@@ -465,6 +460,5 @@ def _create_stimulus(
                 letterHeight=height,
                 size=[.5, .5],
                 pos=stimuli_position,
-                anchor=align_text,
                 alignment=align_text,
             )

bcipy/display/tests/paradigm/rsvp/test_rsvp_display.py

@@ -139,6 +139,7 @@ def test_preview_inquiry_generate_inquiry_preview_fixation(self):
             units='height',
             stimuli_position=self.rsvp.stimuli_pos,
             mode='textbox',
+            align_text='left',
             wrap_width=any()
         ).thenReturn(stim_mock)
 

bcipy/display/tests/test_display.py

@@ -6,7 +6,7 @@
 
 
 class TestInitializeDisplayWindow(unittest.TestCase):
-    """This is Test Case for Initialzing Display Window."""
+    """This is Test Case for Initializing Display Window."""
 
     def setUp(self):
         """Set up needed items for test."""

bcipy/helpers/validate.py

@@ -14,7 +14,7 @@
 from bcipy.gui.alert import confirm
 
 
-def validate_bcipy_session(parameters: dict) -> bool:
+def validate_bcipy_session(parameters: dict, fake_data: bool) -> bool:
     """Check pre-conditions for a BciPy session. If any possible problems are
     detected, alert the user and prompt to continue.
 
@@ -26,7 +26,7 @@ def validate_bcipy_session(parameters: dict) -> bool:
     -------
     True if it's okay to continue, otherwise False
     """
-    possible_alerts = [(parameters['fake_data'], '* Fake data is on.'),
+    possible_alerts = [(fake_data, '* Fake data is on.'),
                        (is_connected(), '* Internet is on.'),
                        (is_battery_powered(), '* Operating on battery power')]
     alert_messages = [

bcipy/main.py

@@ -33,7 +33,8 @@ def bci_main(
         task: TaskType,
         experiment: str = DEFAULT_EXPERIMENT_ID,
         alert: bool = False,
-        visualize: bool = True) -> bool:
+        visualize: bool = True,
+        fake: bool = False) -> bool:
     """BCI Main.
 
     The BCI main function will initialize a save folder, construct needed information
@@ -53,12 +54,17 @@ def bci_main(
         experiment_id (str): Name of the experiment. Default name is DEFAULT_EXPERIMENT_ID.
         alert (bool): whether to alert the user when the task is complete
         visualize (bool): whether to visualize data at the end of a task
+        fake (bool): whether to use fake acquisition data during the session. If None, the
+            fake data will be determined by the parameters file.
     """
     validate_experiment(experiment)
     # Load parameters
     parameters = load_json_parameters(parameter_location, value_cast=True)
 
-    if not validate_bcipy_session(parameters):
+    # cli overrides parameters file for fake data if provided
+    fake = fake if fake is True else parameters['fake_data']
+
+    if not validate_bcipy_session(parameters, fake):
         return False
 
     # Update property to reflect the parameter source
@@ -91,7 +97,7 @@ def bci_main(
     # Collect experiment field data
     collect_experiment_field_data(experiment, save_folder)
 
-    if execute_task(task, parameters, save_folder, alert):
+    if execute_task(task, parameters, save_folder, alert, fake):
         if visualize:
             visualize_session_data(save_folder, parameters)
         return True
@@ -103,7 +109,8 @@ def execute_task(
         task: TaskType,
         parameters: dict,
         save_folder: str,
-        alert: bool) -> bool:
+        alert: bool,
+        fake: bool) -> bool:
     """Execute Task.
 
     Executes the desired task by setting up the display window and
@@ -115,15 +122,14 @@ def execute_task(
         parameters (dict): parameter dictionary
         save_folder (str): path to save folder
         alert (bool): whether to alert the user when the task is complete
+        fake (bool): whether to use fake acquisition data during the session
 
     Returns:
         (bool): True if the task was successfully executed, False otherwise
     """
     signal_model = None
     language_model = None
 
-    fake = parameters['fake_data']
-
     # Init EEG Model, if needed. Calibration Tasks Don't require probabilistic
     # modules to be loaded.
     if task not in TaskType.calibration_tasks():
@@ -202,7 +208,7 @@ def _clean_up_session(
 def bcipy_main() -> None:
     """BciPy Main.
 
-    Command line interface used for running a registered experiment task in Bcipy. To see what
+    Command line interface used for running a registered experiment task in BciPy. To see what
         is available use the --help flag.
     """
     # Needed for windows machines
@@ -228,11 +234,24 @@ def bcipy_main() -> None:
         '--alert',
         default=False,
         action='store_true',
-        help='Alert the user when the task is complete.')
+        help='Alert the user when the session is complete.')
+    parser.add_argument(
+        '-nv',
+        '--noviz',
+        default=True,
+        action='store_false',
+        help='Suppress visuals of the data after the session is complete.')
+    parser.add_argument(
+        '-f',
+        '--fake',
+        default=False,
+        action='store_true',
+        help='Use fake acquisition data for testing.')
     args = parser.parse_args()
 
     # Start BCI Main
-    bci_main(args.parameters, str(args.user), TaskType.by_value(str(args.task)), str(args.experiment), args.alert)
+    bci_main(args.parameters, str(args.user), TaskType.by_value(str(args.task)),
+             str(args.experiment), args.alert, args.noviz, args.fake)
 
 
 if __name__ == '__main__':