Modernize infrastructure

.github/workflows/main.yml

@@ -0,0 +1,47 @@
+name: CI
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+  # Allow rebuilds via API.
+  repository_dispatch:
+    types: rebuild
+
+concurrency:
+  group: run_tests-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@main
+        with:
+          fetch-depth: 0
+
+      - name: Install Conda environment with Micromamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: environment.yml
+          environment-name: mfa
+          create-args: >-
+            python=3.9
+          cache-environment: true
+
+      - name: Download and set up Praat
+        run: |
+          wget https://www.fon.hum.uva.nl/praat/praat6417_linux-intel64-barren.tar.gz -O praat.tar.gz
+          tar -xvzf praat.tar.gz
+          echo "praat=$(pwd)/praat_barren" >> $GITHUB_ENV
+
+      - name: Run tests
+        shell: bash -l {0}
+        run: pytest -x ./tests
+
+      - name: "Upload coverage to Codecov"
+        uses: "codecov/codecov-action@v3"
+        with:
+          file: ./coverage.xml
+          fail_ci_if_error: false

.github/workflows/publish.yml

@@ -0,0 +1,40 @@
+name: Publish Python distributions to PyPI
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  build-n-publish:
+    name: Build and publish to PyPI
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@main
+        with:
+          fetch-depth: 0
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.10"
+
+      - name: Install pypa/build
+        run: >-
+          python -m
+          pip install
+          build
+          --user
+
+      - name: Build a binary wheel and a source tarball
+        run: >-
+          python -m
+          build
+          --sdist
+          --wheel
+          --outdir dist/
+          .
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}

.readthedocs.yaml

@@ -0,0 +1,12 @@
+version: 2
+
+build:
+  os: "ubuntu-20.04"
+  tools:
+    python: "mambaforge-4.10"
+
+sphinx:
+   configuration: docs/source/conf.py
+
+conda:
+  environment: rtd_environment.yml

conch/analysis/amplitude_envelopes/amplitude_envelopes.py

@@ -1,9 +1,7 @@
 import numpy as np
-import librosa
 
 from scipy.signal import filtfilt, butter, hilbert
-
-from librosa import resample
+from scipy.signal import resample
 
 from ..helper import preemphasize
 from ..functions import BaseAnalysisFunction
@@ -62,9 +60,11 @@ def generate_amplitude_envelopes(signal, sr, num_bands, min_frequency, max_frequ
     for i in range(num_bands):
         b, a = butter(2, (band_mins[i] / (sr / 2), band_maxes[i] / (sr / 2)), btype='bandpass')
         env = filtfilt(b, a, proc)
-        env = abs(hilbert(env))
+        env = np.abs(hilbert(env))
         if mode == 'downsample':
-            env = resample(env, sr, 120)
+            env = resample(
+                env, int(env.shape[0] * 120 / sr)
+            )
         envs.append(env)
     envs = np.array(envs).T
     if mode == 'downsample':

conch/analysis/formants/lpc.py

@@ -1,10 +1,10 @@
-import librosa
 import numpy as np
 import scipy as sp
 from scipy.signal import lfilter
 
 from scipy.fftpack import fft, ifft
 from scipy.signal.windows import gaussian
+from scipy.signal import resample
 
 from ..helper import nextpow2
 from ..functions import BaseAnalysisFunction
@@ -216,7 +216,9 @@ def lpc_formants(signal, sr, num_formants, max_freq, time_step,
     alpha = np.exp(-2 * np.pi * 50 * (1 / new_sr))
     proc = lfilter([1., -alpha], 1, signal)
     if sr > new_sr:
-        proc = librosa.resample(proc, sr, new_sr)
+        proc = resample(
+            proc, int(proc.shape[0] * new_sr / sr)
+        )
     nperseg = int(win_len * new_sr)
     nperstep = int(time_step * new_sr)
     if window_shape == 'gaussian':
@@ -237,7 +239,7 @@ def lpc_formants(signal, sr, num_formants, max_freq, time_step,
                 continue
             if f > max_freq - 50:
                 continue
-            formants.append((np.asscalar(f), np.asscalar(bw[j])))
+            formants.append((float(f), float(bw[j])))
         missing = num_formants - len(formants)
         if missing:
             formants += [(None, None)] * missing

environment.yml

@@ -0,0 +1,15 @@
+channels:
+  - conda-forge
+dependencies:
+  - python>=3.8
+  - numpy
+  - librosa
+  - pysoundfile
+  - scipy
+  - praatio
+  - pytest
+  - reaper
+  - pip:
+      - build
+      - twine
+      - pyraat

requirements.txt

@@ -3,8 +3,3 @@ scipy
 pyraat
 praatio
 librosa
-pytest
-sphinx>=1.3b3
-numpydoc
-future
-textgrid

rtd_environment.yml

@@ -0,0 +1,19 @@
+channels:
+  - conda-forge
+dependencies:
+  - python>=3.8
+  - numpy
+  - librosa
+  - pysoundfile
+  - scipy
+  - praatio
+  - sphinx
+  - numpydoc
+  - sphinx-design
+  - sphinx-click
+  - sphinx-intl
+  - pydata-sphinx-theme
+  - myst-parser
+  - mock
+  - pip:
+      - pyraat

tests/conftest.py

@@ -108,22 +108,20 @@ def autovot_correct_times():
 
 @pytest.fixture(scope='session')
 def praatpath():
-    if os.environ.get('TRAVIS'):
+    if os.environ.get('GITHUB_ACTIONS'):
         return os.path.join(os.environ.get('HOME'), 'tools', 'praat')
     return 'praat'
 
 
 @pytest.fixture(scope='session')
 def reaperpath():
-    if os.environ.get('TRAVIS'):
-        return os.path.join(os.environ.get('HOME'), 'tools', 'reaper')
     return 'reaper'
 
 
 @pytest.fixture(scope='session')
 def reaper_func(reaperpath):
     from conch.analysis.pitch.reaper import ReaperPitchTrackFunction
-    return ReaperPitchTrackFunction(reaper_path=reaperpath)
+    return ReaperPitchTrackFunction()
 
 
 @pytest.fixture(scope='session')

tests/test_analysis_autovot.py

@@ -1,13 +1,15 @@
 from conch.analysis.autovot import AutoVOTAnalysisFunction
-import librosa
-from statistics import mean
 import wave
 import pytest
+import shutil
 from conch.analysis.segments import SegmentMapping
 from conch import analyze_segments
 
 
 def test_autovot(acoustic_corpus_path, autovot_markings, classifier_path, autovot_correct_times):
+    autovot_path = shutil.which("VotDecode")
+    if autovot_path is None:
+        pytest.skip("No AutoVOT")
     mapping = SegmentMapping()
     with wave.open(acoustic_corpus_path, 'r') as f: 
         length = f.getnframes() / float(f.getframerate())

tests/test_analysis_formants_praat.py

@@ -2,13 +2,16 @@
     PraatSegmentFormantPointFunction, PraatSegmentFormantTrackFunction
 import librosa
 import pytest
-
+import shutil
 from conch.exceptions import FunctionMismatch
 
 from conch.analysis.segments import FileSegment, SignalSegment, SegmentMapping
 
 
 def test_formant_track_praat(praatpath, base_filenames):
+    praat_path = shutil.which("praat")
+    if praat_path is None:
+        pytest.skip("No Praat")
     for f in base_filenames:
         wavpath = f + '.wav'
         func = PraatFormantTrackFunction(praat_path=praatpath, time_step=0.01,
@@ -24,6 +27,9 @@ def test_formant_track_praat(praatpath, base_filenames):
 
 
 def test_formant_point_praat(praatpath, base_filenames):
+    praat_path = shutil.which("praat")
+    if praat_path is None:
+        pytest.skip("No Praat")
     for f in base_filenames:
         wavpath = f + '.wav'
         func = PraatFormantPointFunction(praat_path=praatpath, time_step=0.01,
@@ -39,6 +45,9 @@ def test_formant_point_praat(praatpath, base_filenames):
 
 
 def test_segment_formant_track_praat(praatpath, acoustic_corpus_path):
+    praat_path = shutil.which("praat")
+    if praat_path is None:
+        pytest.skip("No Praat")
     func = PraatSegmentFormantTrackFunction(praat_path=praatpath, time_step=0.01,
                                      window_length=0.025, num_formants=5, max_frequency=5500)
     segment = FileSegment(acoustic_corpus_path, 2.142, 2.245, 0, padding=0.1)
@@ -55,6 +64,9 @@ def test_segment_formant_track_praat(praatpath, acoustic_corpus_path):
 
 
 def test_segment_formant_point_praat(praatpath, acoustic_corpus_path):
+    praat_path = shutil.which("praat")
+    if praat_path is None:
+        pytest.skip("No Praat")
     func = PraatSegmentFormantPointFunction(praat_path=praatpath, time_step=0.01,
                                      window_length=0.025, num_formants=5, max_frequency=5500, point_percent=0.33)
 

tests/test_analysis_intensity_praat.py

@@ -1,12 +1,16 @@
 from conch.analysis.intensity.praat import PraatIntensityTrackFunction, PraatSegmentIntensityTrackFunction
 import librosa
 import pytest
+import shutil
 
 from conch.analysis.segments import FileSegment, SignalSegment
 from conch.exceptions import FunctionMismatch
 
 
 def test_intensity_praat(praatpath, base_filenames):
+    praat_path = shutil.which("praat")
+    if praat_path is None:
+        pytest.skip("No Praat")
     for f in base_filenames:
         wavpath = f + '.wav'
         func = PraatIntensityTrackFunction(praat_path=praatpath, time_step=0.01)
@@ -22,6 +26,9 @@ def test_intensity_praat(praatpath, base_filenames):
 
 
 def test_segment_pitch_track_praat(praatpath, base_filenames):
+    praat_path = shutil.which("praat")
+    if praat_path is None:
+        pytest.skip("No Praat")
     for f in base_filenames:
         if f != 'acoustic_corpus':
             continue

tests/test_analysis_mfcc_praat.py

@@ -1,10 +1,15 @@
 from conch.analysis.mfcc.praat import PraatMfccFunction
 import librosa
+import shutil
+import pytest
 
 from conch.analysis.segments import FileSegment, SignalSegment
 
 
 def test_mfcc_praat(praatpath, base_filenames):
+    praat_path = shutil.which("praat")
+    if praat_path is None:
+        pytest.skip("No Praat")
     for f in base_filenames:
         wavpath = f + '.wav'
         func = PraatMfccFunction(praat_path=praatpath, window_length=0.025, time_step=0.01, max_frequency=7800,

tests/test_analysis_pitch_praat.py

@@ -1,13 +1,16 @@
 from conch.analysis.pitch.praat import PraatPitchTrackFunction, PraatSegmentPitchTrackFunction
 import librosa
 from statistics import mean
-from scipy.io import wavfile
 import pytest
+import shutil
 from conch.analysis.segments import FileSegment, SignalSegment
 from conch.exceptions import FunctionMismatch
 
 
 def test_pitch_praat(praatpath, base_filenames):
+    praat_path = shutil.which("praat")
+    if praat_path is None:
+        pytest.skip("No Praat")
     for f in base_filenames:
         wavpath = f + '.wav'
         func = PraatPitchTrackFunction(praat_path=praatpath, time_step=0.01,
@@ -22,6 +25,9 @@ def test_pitch_praat(praatpath, base_filenames):
         # assert pitch == pitch2
 
 def test_pitch_pulses_praat(praatpath, noise_path, y_path):
+    praat_path = shutil.which("praat")
+    if praat_path is None:
+        pytest.skip("No Praat")
     func = PraatPitchTrackFunction(praat_path=praatpath, time_step=0.01, min_pitch=75, max_pitch=600,
                                     with_pulses=True)
     pitch, pulses = func(noise_path)
@@ -43,6 +49,9 @@ def test_pitch_pulses_praat(praatpath, noise_path, y_path):
 
 
 def test_segment_pitch_track_praat(praatpath, acoustic_corpus_path):
+    praat_path = shutil.which("praat")
+    if praat_path is None:
+        pytest.skip("No Praat")
     func = PraatSegmentPitchTrackFunction(praat_path=praatpath, time_step=0.01, min_pitch=75, max_pitch=600)
     segment = FileSegment(acoustic_corpus_path, 2.142, 2.245, 0, padding=0.1)
     pitch = func(segment)