CI

.github/workflows/main.yml

@@ -0,0 +1,100 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: BciPy
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - '**'
+
+jobs:
+  build-ubuntu:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [3.7, 3.8]
+
+    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
+      run: |
+        sudo apt-get install libgtk-3-dev
+        sudo apt-get install freeglut3-dev
+        sudo apt-get install freetype*
+        sudo apt-get install portaudio*
+        sudo apt-get install libsndfile*
+        sudo apt-get install xvfb
+        python -m pip install --upgrade pip
+        pip install -r dev_requirements.txt
+        pip install -e .
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 bcipy
+    - name: Unit test
+      run: |
+        xvfb-run coverage run --branch --source=bcipy -m pytest --mpl -k "not slow"
+
+  build-windows:
+
+    runs-on: windows-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [3.7, 3.8]
+
+    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
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r dev_requirements.txt
+        pip install -e .
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 bcipy
+    - name: Unit test
+      run: |
+        coverage run --branch --source=bcipy -m pytest --mpl -k "not slow"
+
+  build-macos:
+
+    runs-on: macos-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [3.7, 3.8]
+
+    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
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r dev_requirements.txt
+        pip install -e .
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 bcipy
+    - name: Unit test
+      run: |
+        coverage run --branch --source=bcipy -m pytest --mpl -k "not slow"

README.md

@@ -1,36 +1,40 @@
-# Brain- Computer Interface Codebase
-------------------------------------
+# BciPy: Brain-Computer Interface Software in Python
 
-### What is it?
 
-It is Brain-computer interface software written in Python. It can function as a standalone or you can take the tools you need and start coding your own system. See our official BciPy documentation including affiliations and more context information here: https://bcipy.github.io/  (in progress).
+[![BciPy](https://github.com/CAMBI-tech/BciPy/actions/workflows/main.yml/badge.svg)](https://github.com/CAMBI-tech/BciPy/actions/workflows/main.yml)
+[![contributions welcome](https://img.shields.io/badge/contributions-welcome-brightgreen.svg)](https://github.com/CAMBI-tech/BciPy/fork)
+[![Follow on Twitter](https://img.shields.io/twitter/follow/cambi_tech?label=Follow&style=social)](https://twitter.com/cambi_tech)
 
-It should, based on our dependencies, work on most recent operating systems, however it has only been verified on Windows (7 & 10 Pro) and Mac OSx (High Sierra & Mojave) at this time. It won't build as is on Linux. Some additional work will be needed to install WxPython and pylsl.
 
-### Contributions Welcome!
+BciPy is a library for conducting Brain-Computer Interface experiments in Python. It functions as a standalone application for experimental data collection or you can take the tools you need and start coding your own system. See our official BciPy documentation including affiliations and more context information [here](https://bcipy.github.io/) (in progress).
 
-This is our first release. It is verified using LSL with DSI and gtec for the Calibration modes only at this time with both image and text stimuli. It comes with a fake data server to help you develop while mocking real time EEG acquisition. We are taking all suggestions at this time for additions, eventually we'll make a contributions wishlist. If you want to be added to the development team, reach out to us and we'll add you to the team slack.
+It will run on the latest windows, linux and macos. Other versions may work as well, but are not guaranteed. To see supported versions and operating systems as of this release see here: [BciPy Builds](https://github.com/CAMBI-tech/BciPy/actions/workflows/main.yml).
 
 *Please cite us when using!*
 
 ```
 Memmott, T., Koçanaoğulları, A., Lawhead, M., Klee, D., Dudy, S., Fried-Oken, M., & Oken, B. (2021). BciPy: brain–computer interface software in Python. Brain-Computer Interfaces, 1-18.
 ```
 
-## Paradigms
------------
+### Contributions Welcome!
 
-*RSVPKeyboard*
+If you want to be added to the development team, reach out to us and we'll add you to the team slack!
 
-```
-	*RSVP KeyboardTM* is an EEG (electroencephalography) based BCI (brain
-		computer interface) typing system. It utilizes a visual presentation technique
-		called rapid serial visual presentation (RSVP). In RSVP, the options are
-		presented rapidly at a single location with a temporal separation. Similarly
-		in RSVP KeyboardTM, the symbols (the letters and additional symbols) are
-		shown at the center of screen. When the subject wants to select a symbol,
-		they await the intended symbol during the presentation and elicit a p300 response to a target symbol.
-```
+### 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/
+
+Other guidelines:
+- All added features require tests and a demo.
+- All tests must pass to merge, even if they are seemingly unrelated to your work.
+- Use Spaces, not Tabs.
+- Use informative names for functions and classes.
+- Document the input and output of your functions / classes in the code. eg in-line commenting and typing
+- Do not push IDE or other local configuration files.
+- All new modules or major functionality should be documented outside of the code with a README.md. 
+	See README.md in repo or go to this site for inspiration: https://github.com/matiassingers/awesome-readme. Always use a Markdown interpreter before pushing. There are many free online or your IDE may come with one.
+
+See this resource for examples: http://docs.python-guide.org/en/latest/writing/style/
 
 ## Dependencies
 ---------------
@@ -40,9 +44,9 @@ This project requires Python > 3.6.5 and other packages defined in the requireme
 ## Installation
 ---------------
 
-#### BCI Setup
+#### BciPy Setup
 
-In order to run BCI suite on your computer, first install **Python 3** [from here.](https://www.python.org/downloads/)
+In order to run BciPy on your computer, first install **Python 3** [from here.](https://www.python.org/downloads/)
 
 You must install Docker and Docker-Machine to use the Language Model developed by CSLU. There are instructions in the language model directory for getting the image you need (think of it as a callable server). You'll also need to download and load the language model [images](https://drive.google.com/drive/folders/1OYpUYASAceb60b2c5obyYytEZ0AZrajY?usp=sharing). If not using or rolling your own, set fake_lm to true in the parameters.json file.
 
@@ -63,7 +67,7 @@ Alternately, if [Make](http://www.mingw.org/) is installed, you may run the foll
 make dev-install
 ```
 
-## Usage Locally
+#### 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.
 
@@ -75,17 +79,37 @@ 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
+##### Example usage as a package
 
 ```python
 from bcipy.helpers import system_utils
 system_utils.get_system_info()
 ```
 
-## Modules and Vital Functions
-------------------------------
+## Glossary
+-----------
+
+***Stimuli***: A single letter, tone or image shown (generally in an inquiry). Singular = stimulus, plural = stimuli.
+
+***Trial***: A collection of data after a stimuli is shown. A----
 
-This a list of the major modules and their functionality. Each module will contain its own README, demo and test scripts. Please check them out for more information!
+***Inquiry***: The set of stimuli after a fixation cross in a spelling task to gather user intent. A ---- B --- C ----
+
+***Series***: Each series contains at least one inquiry. A letter/icon decision is made after a series in a spelling task.
+
+***Session***: Data collected for a task. Comprised of metadata about the task and a list of Series.
+
+***Task***: An experimental design with stimuli, trials, inquiries and series for use in BCI. For instance, "RSVP Calibration" is a task.
+
+***Mode***: Common design elements between task types. For instance, Calibration and Free Spelling are modes.
+
+***Paradigm***: Display paradigm with unique properties and modes. Ex. Rapid-Serial Visual Presentation (RSVP), Matrix Speller, Steady-State Visual Evoked Potential (SSVEP).
+
+
+## Core Modules
+---------------
+
+This a list of the major modules and their functionality. Each module will contain its own README, demo and tests. Please check them out for more information!
 
 - `acquisition`: acquires data, gives back desired time series, saves to file at end of session.
 - `display`: handles display of stimuli on screen and passes back stimuli timing.
@@ -99,36 +123,35 @@ This a list of the major modules and their functionality. Each module will conta
 - `feedback`: feedback mechanisms for sound and visual stimuli.
 - `main`: executor of experiments. Main entry point into the application
 
-## Demo and Tests
------------------
 
-All major functions and modules have demo and test files associated with them which may be run locally. This should help orient you to the functionality as well as serve as documentation. *If you add to the repo, you should be adding tests and fixing any test that fail when you change the code.*
+## Paradigms
+------------
 
-For example, you may run the main BciPy demo by:
 
-`python demo/bci_main_demo.py`
+> RSVPKeyboard
 
-This demo will load in parameters and execute a demo task defined in the file. There are demo files for all modules listed above except language_model, helpers, and utils. Run them as a python script!
 
-This repository uses pytest for execution of tests. You may execute them by:
+```
+*RSVP KeyboardTM* is an EEG (electroencephalography) based BCI (brain
+	computer interface) typing system. It utilizes a visual presentation technique
+	called rapid serial visual presentation (RSVP). In RSVP, the options are
+	presented rapidly at a single location with a temporal separation. Similarly
+	in RSVP KeyboardTM, the symbols (the letters and additional symbols) are
+	shown at the center of screen. When the subject wants to select a symbol,
+	they await the intended symbol during the presentation and elicit a p300 response to a target symbol.
+```
 
-`py.test` or `pytest` depending on your OS
+## Demo
+--------
 
-## Contribution Guidelines
---------------------------
+All major functions and modules have demo and test files associated with them which may be run locally. This should help orient you to the functionality as well as serve as documentation. *If you add to the repo, you should be adding tests and fixing any test that fail when you change the code.*
 
-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/
+For example, you may run the main BciPy demo by:
 
-1. All added code will need tests and a demo (if a large feature).
-2. All tests must pass to merge, even if they are seemingly unrelated to your task.
-3. Pull requests must be tested locally and by the requester on a different computer.
-4. Use Spaces, not Tabs.
-5. Use informative names for functions and classes.
-6. Document the input and output of your functions / classes in the code. eg in-line commenting
-7. Do not push IDE or other local configuration files.
-8. All new modules or major functionality should be documented outside of the code with a README.md. See README.md in repo or go to this site for inspiration: https://github.com/matiassingers/awesome-readme. Always use a Markdown interpreter before pushing. There are many free online or your IDE may come with one.
+`python demo/bci_main_demo.py`
+
+This demo will load in parameters and execute a demo task defined in the file. There are demo files for all modules listed above except language_model, helpers, and utils. Run them as a python script!
 
-Use this resource for examples: http://docs.python-guide.org/en/latest/writing/style/
 
 ## Testing
 ----------
@@ -169,6 +192,7 @@ make coverage-html
 ```
 
 ## Linting
+----------
 
 This project enforces `PEP` style guidelines using [flake8](http://flake8.pycqa.org/en/latest/).
 
@@ -190,39 +214,9 @@ Alternately, if Make is installed, you may run the follow command to run autopep
 make lint
 ```
 
-## Glossary
------------
-
-***Stimuli***: A single letter, tone or image shown (generally in an inquiry). Singular = stimulus, plural = stimuli.
-
-***Trial***: A collection of data after a stimuli is shown. A----
-
-***Inquiry***: The set of stimuli after a fixation cross in a spelling task to gather user intent. A ---- B --- C ----
-
-***Series***: Each series contains at least one inquiry. A letter/icon decision is made after a series in a spelling task.
-
-***Session***: Data collected for a task. Comprised of metadata about the task and a list of Series.
-
-***Task***: An experimental design with stimuli, trials, inquiries and series for use in BCI. For instance, "RSVP Calibration" is a task.
-
-***Mode***: Common design elements between task types. For instance, Calibration and Free Spelling are modes.
-
-***Paradigm***: Display paradigm with unique properties and modes. Ex. Rapid-Serial Visual Presentation (RSVP), Matrix Speller, Steady-State Visual Evoked Potential (SSVEP).
-
-
-## Authorship
---------------
+## Contributors
+---------------
 
-- Tab Memmott (OHSU)
-- Matthew Lawhead (OHSU)
-- Aziz Kocanaogullari (NEU)
-- Shiran Dudy (OHSU)
-- Dani Smektala (OHSU)
-- Ian Jackson (Reed)
-- Alister Cedeño (OHSU)
-- Berkan Kadioglu (NEU)
-- Basak Celik (NEU)
-- Niklas Smedemark-Margulies (NEU) 
-- Andac Demir (NEU)
-- Shaobin Xu (NEU)
+All contributions are greatly appreciated!
 
+[![image of contributors generated by https://contributors-img.web.app/ pulling from https://github.com/CAMBI-tech/BciPy/graphs/contributors](https://contrib.rocks/image?repo=CAMBI-tech/BciPy)](https://github.com/CAMBI-tech/BciPy/graphs/contributors)

bcipy/acquisition/tests/protocols/lsl/test_lsl_device.py

@@ -149,7 +149,7 @@ def test_with_trigger_channel(self):
 
         device.connect()
         device.acquisition_init()
-        self.assertEquals(self.channels, device.channels)
+        self.assertEqual(self.channels, device.channels)
 
     def test_with_marker_stream(self):
         server = LslDataServer(device_spec=self.device_spec, add_markers=True)
@@ -158,8 +158,8 @@ def test_with_marker_stream(self):
 
         device.connect()
         device.acquisition_init()
-        self.assertEquals(self.channels, device.channels)
-        self.assertEquals(len(self.channels), len(device.read_data()))
+        self.assertEqual(self.channels, device.channels)
+        self.assertEqual(len(self.channels), len(device.read_data()))
 
     def test_with_marker_stream_included(self):
         server = LslDataServer(device_spec=self.device_spec, add_markers=True)
@@ -170,9 +170,9 @@ def test_with_marker_stream_included(self):
 
         device.connect()
         device.acquisition_init()
-        self.assertEquals(self.channels + [MARKER_STREAM_NAME],
-                          device.channels)
-        self.assertEquals(len(self.channels) + 1, len(device.read_data()))
+        self.assertEqual(self.channels + [MARKER_STREAM_NAME],
+                         device.channels)
+        self.assertEqual(len(self.channels) + 1, len(device.read_data()))
 
     def test_with_marker_stream_and_timestamp(self):
         server = LslDataServer(device_spec=self.device_spec, add_markers=True)
@@ -184,9 +184,9 @@ def test_with_marker_stream_and_timestamp(self):
 
         device.connect()
         device.acquisition_init()
-        self.assertEquals(self.channels + [LSL_TIMESTAMP, MARKER_STREAM_NAME],
-                          device.channels)
-        self.assertEquals(len(self.channels) + 2, len(device.read_data()))
+        self.assertEqual(self.channels + [LSL_TIMESTAMP, MARKER_STREAM_NAME],
+                         device.channels)
+        self.assertEqual(len(self.channels) + 2, len(device.read_data()))
 
     def test_renaming_columns(self):
         server = LslDataServer(device_spec=self.device_spec,
@@ -205,8 +205,8 @@ def test_renaming_columns(self):
             'C3', 'C4', 'Cz', 'FPz', 'POz', 'CPz', 'O1', 'O2',
             'TRG_device_stream', 'TRG'
         ]
-        self.assertEquals(expected, device.channels)
-        self.assertEquals(expected, device.device_info.channels)
+        self.assertEqual(expected, device.channels)
+        self.assertEqual(expected, device.device_info.channels)
 
 
 if __name__ == '__main__':

bcipy/helpers/tests/test_session.py

@@ -25,7 +25,7 @@ def tearDown(self):
     def test_session_data(self):
         """Test session_data method outputs letters with evidence."""
         data = session_data(data_dir=self.data_dir)
-        self.assertEquals(data["total_number_series"], 2)
+        self.assertEqual(data["total_number_series"], 2)
         self.assertTrue("A" in data["series"]["1"]["0"]["likelihood"])
         self.assertTrue("B" in data["series"]["1"]["0"]["likelihood"])