Report artifact enhancements, README, Python 3.10.6 support

.coveragerc

@@ -2,12 +2,15 @@
 [run]
 omit =
         *__init__*
+        *__main__*
         */usr/local/lib*
         *tests*
         *test*
         *demo*
         *exceptions.py
-        */gui/*
+        */gui/experiments/*
+        */gui/viewer/*
+        */gui/BCInterface.py
 
 [report]
 exclude_lines =

.github/workflows/main.yml

@@ -18,7 +18,7 @@ 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
@@ -68,7 +68,7 @@ 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
@@ -103,7 +103,7 @@ 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@v4

README.md

@@ -40,7 +40,8 @@ If using zsh, instead of bash, you may encounter a segementation fault when runn
 ## Installation
 ---------------
 
-#### BciPy Setup
+### BciPy Setup
+----------------
 
 In order to run BciPy on your computer, after following the dependencies above, you will need to install the BciPy package.
 
@@ -62,26 +63,86 @@ Alternately, if [Make](http://www.mingw.org/) is installed, you may run the foll
 make dev-install
 ```
 
-#### Client Usage
-   	Invoke an experiment protocol or task directly using command line utility `bcipy`.
-		- You can pass it attributes with flags, if desired.
-				Running with a User ID and Task: `bcipy --user "bci_user" --task "RSVP Calibration"`
-				Running with a User ID and Tasks with a registered Protocol: `bcipy --user "bci_user" --experiment "default"`
-				Running with fake data: `bcipy --fake`
-				Running without visualizations: `bcipy --noviz`
-				Running with alerts after each Task execution: `bcipy --alert`
-				Running with custom parameters: `bcipy --parameters "path/to/valid/parameters.json"`
+### Client Usage
+----------------
+
+##### Run an experiment protocol or task
+
+Invoke an experiment protocol or task directly using command line utility `bcipy`.
+
+- Use the help flag to see other available input options: `bcipy --help`
+	- You can pass it attributes with flags, if desired.
+		- Running with a User ID and Task: 
+    		- `bcipy --user "bci_user" --task "RSVP Calibration"`
+		- Running with a User ID and Tasks with a registered Protocol: 
+    		- `bcipy --user "bci_user" --experiment "default"`
+		- Running with fake data: 
+    		- `bcipy --fake`
+		- Running without visualizations: 
+    		- `bcipy --noviz`
+		- Running with alerts after each Task execution: 
+    		- `bcipy --alert`
+		- Running with custom parameters: 
+    		- `bcipy --parameters "path/to/valid/parameters.json"`
+
+##### Train a signal model with registered BciPy models
+
+To train a signal model (currently `PCARDAKDE`), run the following command after installing BciPy:
+
+`bcipy-train`
+
+- Use the help flag to see other available input options: `bcipy-train --help`
+	- You can pass it attributes with flags, if desired.
+		- Running without a window prompting for data session folder: 
+			- `bcipy-train -d path/to/data`
+		- Running with data visualizations (ERPs, etc.): 
+			- `bcipy-train -v`
+    	- Running with data visualizations that do not show, but save to file: 
+			- `bcipy-train -s`
+       - Running with balanced accuracy:
+           - `bcipy-train --balanced-acc`
+		- Running with alerts after each Task execution: 
+			- `bcipy-train --alert`
+		- Running with custom parameters: 
+			- `bcipy-train -p "path/to/valid/parameters.json"`
+
+##### Visualize ERP data from a session with Target / Non-Target labels
+
+To generate plots that can be shown or saved after collection of data, run the following command after installing BciPy:
+
+`bcipy-erp-viz`
+
+- Use the help flag to see other available input options: `bcipy-erp-viz --help`
+	- You can pass it attributes with flags, if desired.
+		- Running without a window prompting for data session folder: 
+			- `bcipy-erp-viz -s path/to/data`
+		- Running with data visualizations (ERPs, etc.): 
+			- `bcipy-erp-viz --show`
+		- Running with data visualizations that do not show, but save to file: 
+			- `bcipy-erp-viz --save`
+		- Running with custom parameters (default is in bcipy/parameters/parameters.json): 
+			- `bcipy-erp-viz -p "path/to/valid/parameters.json"`
+
+##### BciPy Simulator Usage
+
+The simulator can be run using the command line utility `bcipy-sim`.
+
+Ex. 
+`bcipy-sim -d my_data_folder/ -p my_parameters.json -m my_models/ -n 5`
+
+Run `bcipy-sim --help` for documentation or see the README in the simulator module.
 
-		- Use the help flag to see other available input options: `bcipy --help`
 
-#####  Example Usage as a Package
+###  Package Usage
+-------------------
 
 ```python
 from bcipy.helpers import system_utils
 system_utils.get_system_info()
 ```
 
-#### Example Usage through the GUI
+### GUI Usage
+-------------
 
 Run the following command in your terminal to start the BciPy GUI:
 ```sh
@@ -95,16 +156,6 @@ make bci-gui
 ```
 
 
-#### Simulator Usage
-
-The simulator can be run using the command line utility `bcipy-sim`.
-
-Ex. 
-`bcipy-sim -d my_data_folder/ -p my_parameters.json -m my_models/ -n 5`
-
-Run `bcipy-sim --help` for documentation or see the README in the simulator module.
-
-
 ## Glossary
 -----------
 
@@ -150,7 +201,7 @@ This a list of the major modules and their functionality. Each module will conta
 ## Paradigms
 ------------
 
-See `bcipy/task/README.md` for more information on all supported paradigms and modes. The following are the supported and validated paradigms:
+See `bcipy/task/README.md` for more information on all supported paradigms, tasks, actions and modes. The following are the supported and validated paradigms:
 
 
 > RSVPKeyboard
@@ -213,7 +264,6 @@ After running the above command, the recommended offset correction value will be
 ```bash
 # Let's say the recommneded offset value is 0.1
 python bcipy/helpers/offset.py --offset "0.1" -p
-
 ```
 
 Alternately, if Make is installed, you may run the follow command to run offset determination and display the results:
@@ -306,10 +356,11 @@ make type
 
 
 ### Contributions Welcome!
+--------------------------
 
 If you want to be added to the development team slack or have additional questions, please reach out to us at [email protected]!
 
-### Contribution Guidelines
+#### Contribution Guidelines
 
 We follow and will enforce the contributor's covenant to foster a safe and inclusive environment for this open source software, please reference this link for more information: https://www.contributor-covenant.org/
 
@@ -325,7 +376,7 @@ Other guidelines:
 
 See this resource for examples: http://docs.python-guide.org/en/latest/writing/style/
 
-## Contributors
+### Contributors
 ---------------
 
 All contributions are greatly appreciated!

bcipy/gui/file_dialog.py

@@ -15,7 +15,7 @@ class FileDialog(QWidget):
 
     def __init__(self):
         super().__init__()
-        self.title = 'PyQt6 file dialogs - pythonspot.com'
+        self.title = 'File Dialog'
         self.width = 640
         self.height = 480
 
@@ -45,20 +45,23 @@ def ask_file(self,
                                                   options=self.options)
         return filename
 
-    def ask_directory(self, directory: str = "") -> str:
+    def ask_directory(self, directory: str = "", prompt: str = "Select Directory") -> str:
         """Opens a dialog window to select a directory.
 
         Returns
         -------
         path or None
         """
         return QFileDialog.getExistingDirectory(self,
-                                                "Select Directory",
+                                                prompt,
                                                 directory=directory,
                                                 options=self.options)
 
 
-def ask_filename(file_types: str = DEFAULT_FILE_TYPES, directory: str = "", prompt="Select File") -> str:
+def ask_filename(
+        file_types: str = DEFAULT_FILE_TYPES,
+        directory: str = "",
+        prompt: str = "Select File") -> str:
     """Prompt for a file.
 
     Parameters
@@ -87,7 +90,7 @@ def ask_filename(file_types: str = DEFAULT_FILE_TYPES, directory: str = "", prom
     return filename
 
 
-def ask_directory() -> str:
+def ask_directory(prompt: str = "Select Directory") -> str:
     """Prompt for a directory.
 
     Returns
@@ -100,9 +103,10 @@ def ask_directory() -> str:
     directory = ''
     if preferences.last_directory:
         directory = str(Path(preferences.last_directory).parent)
-    name = dialog.ask_directory(directory)
+    name = dialog.ask_directory(directory, prompt=prompt)
     if name and Path(name).is_dir():
         preferences.last_directory = name
+
     # Alternatively, we could use `app.closeAllWindows()`
     app.quit()
 

bcipy/helpers/convert.py

@@ -498,7 +498,7 @@ def convert_to_mne(
         channel_types: Optional[List[str]] = None,
         transform: Optional[Composition] = None,
         montage: str = 'standard_1020',
-        volts: bool = True) -> RawArray:
+        volts: bool = False) -> RawArray:
     """Convert to MNE.
 
     Returns BciPy RawData as an MNE RawArray. This assumes all channel names

bcipy/helpers/stimuli.py

@@ -433,12 +433,19 @@ def mne_epochs(mne_data: RawArray,
     tmp_data.set_annotations(all_annotations)
 
     events_from_annot, _ = mne.events_from_annotations(tmp_data)
+
+    if baseline is None:
+        baseline = (0, 0)
+        tmin = -0.1
+    else:
+        tmin = baseline[0]
+
     return Epochs(
         mne_data,
         events_from_annot,
         baseline=baseline,
         tmax=trial_length,
-        tmin=-0.05,
+        tmin=tmin,
         proj=False,  # apply SSP projection to data. Defaults to True in Epochs.
         reject_by_annotation=reject_by_annotation,
         preload=preload)

bcipy/helpers/tests/test_convert.py

@@ -528,7 +528,7 @@ def test_convert_to_mne_with_transform(self):
         def transform(x, fs):
             return x * multiplier, fs
 
-        data = convert_to_mne(self.raw_data, transform=transform)
+        data = convert_to_mne(self.raw_data, transform=transform, volts=True)
 
         self.assertTrue(len(data) > 0)
         self.assertEqual(data.ch_names, self.channels[1:])

bcipy/helpers/visualization.py

@@ -87,7 +87,7 @@ def visualize_erp(
     trial_length = trial_window[1] - 0.0
 
     # check for a baseline interval or set to None
-    if trial_window[0] < 0:
+    if trial_window[0] <= 0:
         baseline = (trial_window[0], 0.0)
     else:
         baseline = None