fix: Fixes env, adds testing

.github/workflows/env_test.yml

@@ -8,7 +8,7 @@ jobs:
  matrix:
  os: [ubuntu-20.04, ubuntu-22.04, windows-latest, macos-12, macos-11]
  python-version: ["3.8", "3.9"]
- runs-on: ${{ matrix.os }}
+ runs-on: pyth
  steps:
  - uses: actions/checkout@v3
  - uses: actions/setup-python@v4
@@ -18,3 +18,6 @@ jobs:
  run: |
  python -m pip install --upgrade pip poetry
  poetry install
+ - name: Run test
+ run: |
+ python -m pytest pyha_tests

.gitignore

@@ -308,4 +308,5 @@ $RECYCLE.BIN/
 # Windows shortcuts
 *.lnk
 
-# End of https://www.toptal.com/developers/gitignore/api/jupyternotebooks,python,linux,macos,windows,visualstudiocode
+# End of https://www.toptal.com/developers/gitignore/api/jupyternotebooks,python,linux,macos,windows,visualstudiocode
+credentials.json

.vscode/settings.json

@@ -0,0 +1,7 @@
+{
+ "python.testing.pytestArgs": [
+ "pyha_tests"
+ ],
+ "python.testing.unittestEnabled": false,
+ "python.testing.pytestEnabled": true
+}

pyha_tests/test_pyha.py

@@ -0,0 +1,78 @@
+'''Tests PyHa environment
+'''
+import json
+import os
+from pathlib import Path
+from tempfile import TemporaryDirectory
+from typing import Dict
+
+import pytest
+from nas_unzip.nas import nas_unzip
+
+from PyHa.IsoAutio import generate_automated_labels
+
+
+@pytest.fixture(name='creds')
+def create_creds() -> Dict[str, str]:
+ """Obtains the credentials
+
+ Returns:
+ Dict[str, str]: Username and password dictionary
+ """
+ if Path('credentials.json').is_file():
+ with open('credentials.json', 'r', encoding='ascii') as handle:
+ return json.load(handle)
+ else:
+ value = os.environ['NAS_CREDS'].splitlines()
+ assert len(value) == 2
+ return {
+ 'username': value[0],
+ 'password': value[1]
+ }
+
+
+def test_pyha(creds):
+ """Tests PyHa
+ """
+ with TemporaryDirectory() as path:
+ nas_unzip(
+ network_path='smb://e4e-nas.ucsd.edu:6021/temp/github_actions/pyha/pyha_test.zip',
+ output_path=Path(path),
+ username=creds['username'],
+ password=creds['password']
+ )
+ isolation_parameters = {
+ "model": "tweetynet",
+ "tweety_output": True,
+ "technique": "steinberg",
+ "threshold_type": "median",
+ "threshold_const": 2.0,
+ "threshold_min": 0.0,
+ "window_size": 2.0,
+ "chunk_size": 5.0,
+ "verbose": True
+ }
+ generate_automated_labels(path, isolation_parameters)
+ isolation_parameters = {
+ "model": "birdnet",
+ "output_path": "outputs",
+ "lat": 35.4244,
+ "lon": -120.7463,
+ "week": 18,
+ "min_conf": 0.1,
+ "filetype": "wav",
+ "num_predictions": 1,
+ "write_to_csv": False,
+ }
+ generate_automated_labels(path, isolation_parameters)
+ isolation_parameters = {
+ "model": "microfaune",
+ "technique": "steinberg",
+ "threshold_type": "median",
+ "threshold_const": 2.0,
+ "threshold_min": 0.0,
+ "window_size": 2.0,
+ "chunk_size": 5.0,
+ "verbose": True
+ }
+ generate_automated_labels(path, isolation_parameters)

pyproject.toml

@@ -28,6 +28,9 @@ build-backend = "poetry.core.masonry.api"
 [tool.poetry.group.dev.dependencies]
 pylint = "^3.0.2"
 pytest = "^7.4.3"
+nas_unzip = { git="https://github.com/UCSD-E4E/synology-download.git", rev="dcca086" }
+synology-api = "0.5.1"
+autopep8 = "^2.0.4"
 
 [tool.poetry.dependencies]
 python = ">=3.8,<3.10"
@@ -36,13 +39,13 @@ jupyter = "^1.0.0"
 scikit-learn = "^1.3.2"
 seaborn = "^0.13.0"
 keras = "^2.8.0"
-pandas = "^1.2.3"
+pandas = "^2.0.0"
 matplotlib = "^3.4.1"
 scipy = "^1.6.2"
 torch = "^2.1.0"
 tensorflow = {version = "^2.13.0" }
 tensorflow-macos = { version = "^2.13.0", platform = "darwin", markers = "platform_machine=='arm64'" }
-tensorflow-intel = { version = "^2.13.0", platform = "win32" }
+tensorflow-intel = { version = "2.13.0", platform = "win32" }
 tensorflow-cpu = [
  { version = "^2.13.0", platform = "linux", markers = "platform_machine!='arm64' and platform_machine!='aarch64'" },
  { version = "^2.13.0", platform = "darwin", markers = "platform_machine!='arm64' and platform_machine!='aarch64'" },