Update to use pyproject.toml (#367)

.github/workflows/main.yml

@@ -79,10 +79,6 @@ jobs:
     - name: update pip & install custom dependencies
       run: |
         python -m pip install --upgrade pip
-    - name: install manually downloaded pyWinhook wheel for Python 3.9
-      if: matrix.python-version == 3.9
-      run: |
-        pip install ./.bcipy/downloads/pyWinhook-1.6.2-cp39-cp39-win_amd64.whl
     - name: install dependencies
       run: |
         make dev-install
@@ -96,6 +92,9 @@ jobs:
     - name: lint
       run: |
         make lint
+    - name: build
+      run: |
+        make build
 
   build-macos:
 
@@ -123,11 +122,17 @@ jobs:
       if: always()
       run: |
         make coverage-report
+        make coverage-xml
     - name: type-check
       run: |
         make type
     - name: lint
       run: |
         make lint
-
-    
+    - 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"

.gitignore

@@ -11,6 +11,7 @@ mypy-html.css
 index.html
 htmlcov/
 html/
+*.xml
 
 # Virtualenv
 venv/

Makefile

@@ -2,11 +2,13 @@ install:
 	pip install -e .
 
 dev-install:
-	pip install -r dev_requirements.txt
-	pip install psychopy==2024.2.1 --no-deps
-	pip install kenlm==0.1 --global-option="--max_order=12"
+	pip install -e ".[dev]"
 	make install
 
+build:
+	pip install -e ".[release]"
+	python -m build --sdist --wheel
+
 test-all:
 	make coverage-report
 	make type
@@ -19,18 +21,21 @@ integration-test:
 	pytest --mpl -k "slow"
 
 coverage-report:
-	coverage run --branch --source=bcipy -m pytest --mpl -k "not slow"
+	coverage run --branch -m pytest --mpl -k "not slow"
 	coverage report
 
+coverage-xml:
+	coverage xml -o "cobertura.xml"
+
 coverage-html:
-	coverage run --branch --source=bcipy -m pytest --mpl -k "not slow"
+	coverage run --branch -m pytest --mpl -k "not slow"
 	coverage html
 
 lint:
 	flake8 bcipy
 
 lint-fix:
-	autopep8 --in-place --aggressive -r bcipy
+	autopep8 --in-place --aggressive --max-line-length 120 --ignore "E402,E226,E24,W50,W690" -r bcipy
 	flake8 bcipy
 
 type:
@@ -43,6 +48,15 @@ clean:
 	find . -name "*.py[co]" -o -name __pycache__ -exec rm -rf {} +
 	find . -path "*/*.pyo"  -delete
 	find . -path "*/*.pyc"  -delete
+	find . -path "*/*/__pycache__"  -delete
+	rm -rf .pytest_cache
+	rm -rf .mypy_cache
+	rm -rf .coverage
+	rm -rf htmlcov
+	rm -rf dist
+	rm -rf build
+	rm -rf bcipy.egg-info
+	rm -rf bcipy_cache
 
 bci-gui:
 	python bcipy/gui/BCInterface.py

README.md

@@ -2,13 +2,14 @@
 
 
 [![BciPy](https://github.com/CAMBI-tech/BciPy/actions/workflows/main.yml/badge.svg)](https://github.com/CAMBI-tech/BciPy/actions/workflows/main.yml)
+[![Codacy Badge](https://app.codacy.com/project/badge/Grade/96e31da4b0554dae9db7a1356556b0d5)](https://app.codacy.com/gh/CAMBI-tech/BciPy/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade)
 [![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)
 
 
 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/).
 
-It will run on the latest windows (7, 10, 11), linux (ubuntu 22.04) and macos (Big Sur). 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).
+It will run on the latest windows (10, 11), linux (ubuntu 22.04) and macos (Sonoma). 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!*
 
@@ -18,7 +19,7 @@ Memmott, T., Koçanaoğulları, A., Lawhead, M., Klee, D., Dudy, S., Fried-Oken,
 
 ## Dependencies
 ---------------
-This project requires Python 3.8 or 3.9. Please see notes below for additional OS specific dependencies before installation can be completed and reference our documentation/FAQs for more information: https://bcipy.github.io/hardware-os-config/
+This project requires Python 3.8, 3.9 or 3.10. Please see notes below for additional OS specific dependencies before installation. See our documentation/FAQs for more information [here](https://bcipy.github.io/hardware-os-config/).
 
 ### Linux
 
@@ -28,8 +29,6 @@ You will need to install the prerequisites defined in `scripts\shell\linux_requi
 
 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
 
@@ -48,9 +47,8 @@ In order to run BciPy on your computer, after following the dependencies above,
 To install for use locally and use of the GUI:
 1. Git clone https://github.com/BciPy/BciPy.git
 2. Change directory in your terminal to the repo directory.
-3. Install the kenlm language model package. `pip install kenlm==0.1 --global-option="--max_order=12"`.
-4. Install PsychoPy with no dependencies. `pip install psychopy==2023.2.1 --no-deps`.
-5. Install BciPy in development mode. `pip install -e .`
+3. [Optional] Install the kenlm language model package. `pip install kenlm==0.1 --global-option="--max_order=12"`.
+4. Install BciPy in development mode. `pip install -e .`
 
 
 If wanting the latest version from PyPi and to build using modules:
@@ -356,6 +354,45 @@ Alternately, if Make is installed, you may run the follow command to run mypy:
 make type
 ```
 
+## Release
+----------
+
+The process to release a new version of BciPy is done through the below steps. An admin PyPi account is required to upload the package with a valid token. An admin GitHub account is also required to create tag the release. Reach out to the development team for more information.
+
+### Install release dependencies and create a universal wheel
+
+Configuration for the distribution is in `pyproject.toml`. To create a universal wheel, run:
+
+
+```sh
+pip install -e ".[release]"
+python -m build --sdist --wheel
+```
+
+Alternately, if Make is installed, you may run the follow command to build the wheel:
+
+```sh
+make build
+```
+
+### Upload to PyPi
+
+To upload the package to [PyPi](https://pypi.org/project/bcipy/), run:
+
+```sh
+twine upload dist/*
+```
+
+### Tag the release on GitHub
+
+```sh
+git tag v*add_version*
+git push --tags'
+```
+
+### Create GitHub Release
+
+Using the tag you just created, create a release on GitHub. Include the release notes from the CHANGELOG in the description. See https://github.com/CAMBI-tech/BciPy/releases for examples.
 
 ### Contributions Welcome!
 --------------------------

bcipy/core/session.py

@@ -1,10 +1,10 @@
+# mypy: disable-error-code="arg-type"
 """Helper functions for managing and parsing session.json data."""
 import csv
 import itertools
 import json
 import os
 import sqlite3
-import subprocess
 from dataclasses import dataclass, fields
 from typing import Any, Dict, List, Optional
 
@@ -16,12 +16,10 @@
 BLACK = COLOR_INDEX[0]
 WHITE = COLOR_INDEX[1]
 YELLOW = COLOR_INDEX[5]
-from bcipy.config import (BCIPY_ROOT, DEFAULT_ENCODING,
-                          DEFAULT_PARAMETERS_FILENAME, EXPERIMENT_DATA_FILENAME,
+from bcipy.config import (DEFAULT_ENCODING,
+                          DEFAULT_PARAMETERS_FILENAME,
                           SESSION_DATA_FILENAME, SESSION_SUMMARY_FILENAME)
-from bcipy.io.load import (load_experiment_fields, load_experiments,
-                           load_json_parameters)
-from bcipy.helpers.validate import validate_field_data_written
+from bcipy.io.load import load_json_parameters
 from bcipy.task.data import Session
 
 
@@ -45,21 +43,6 @@ def session_data(data_dir: str) -> Dict:
     return data
 
 
-def collect_experiment_field_data(experiment_name: str,
-                                  save_path: str,
-                                  file_name: str = EXPERIMENT_DATA_FILENAME) -> None:
-    experiment = load_experiments()[experiment_name]
-    experiment_fields = load_experiment_fields(experiment)
-
-    if experiment_fields:
-        cmd = (f'python {BCIPY_ROOT}/gui/experiments/ExperimentField.py -e'
-               f' "{experiment_name}" -p "{save_path}" -f "{file_name}"')
-        subprocess.check_call(cmd, shell=True)
-        # verify data was written before moving on
-        if not validate_field_data_written(save_path, file_name):
-            raise Exception('Field data not collected!')
-
-
 @dataclass(frozen=True)
 class EvidenceRecord:
     """Record summarizing Inquiry evidence."""

bcipy/helpers/offset.py

@@ -111,6 +111,7 @@ def calculate_latency(raw_data: RawData,
         if value < 1 and diode_enc:
             diode_enc = False
 
+    trigger_diodes_timestamps = []
     # Plot triggers.txt data if present; vertical line for each value.
     if triggers:
         trigger_diodes_timestamps = [

bcipy/task/demo/control/demo_handler.py

@@ -39,8 +39,6 @@ def _demo_decision_maker():
 
     conjugator = EvidenceFusion(evidence_names, len_dist=len_alp)
     decision_maker = DecisionMaker(
-        min_num_inq=1,
-        max_num_inq=10,
         state='',
         alphabet=alp)