Merge pull request #55 from FastTrackiverse/dev

v0.3.1

.devcontainer/devcontainer.json

@@ -0,0 +1,42 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/python
+{
+	"name": "Python 3",
+	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
+	"image": "mcr.microsoft.com/devcontainers/python:1-3.11",
+	"features": {
+		"ghcr.io/rocker-org/devcontainer-features/quarto-cli:1": {
+			"version": "latest"
+		},
+		"ghcr.io/devcontainers-contrib/features/poetry:2": {
+			"version": "latest"
+		}
+	},
+
+	// Features to add to the dev container. More info: https://containers.dev/features.
+	// "features": {},
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Use 'postCreateCommand' to run commands after the container is created.
+	"postCreateCommand": "poetry install",
+
+	// Configure tool-specific properties.
+	"customizations": {
+		"vscode": {
+			"extensions":
+			["ms-toolsai.jupyter", 
+			"ms-python.vscode-pylance",
+			"njpwerner.autodocstring"],
+			"settings": {"python.testing.pytestArgs": [
+				"tests"
+			],
+			"python.testing.unittestEnabled": false,
+			"python.testing.pytestEnabled": true}
+		}
+	}
+
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+	// "remoteUser": "root"
+}

.github/workflows/test-and-run.yml

@@ -22,7 +22,7 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
         cache: "pip"
@@ -41,6 +41,6 @@ jobs:
       run: |
         python -m pytest --cov=./ --cov-report=xml tests/
     - name: Upload coverage reports to Codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       env:
         CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -160,4 +160,5 @@ cython_debug/
 #.idea/
 
 .vscode
-poetry.lock
+poetry.lock
+.DS_Store

CITATION.cff

@@ -0,0 +1,26 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: fasttrackpy
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - given-names: Josef
+    family-names: Fruehwald
+    orcid: 'https://orcid.org/0000-0001-8480-9461'
+    affiliation: University of Kentucky
+  - given-names: Santiago
+    family-names: Barreda
+    affiliation: UC Davis
+    orcid: 'https://orcid.org/0000-0002-1552-083X'
+identifiers:
+  - type: doi
+    value: 10.5281/zenodo.10212100
+    description: zenodo
+repository-code: 'https://github.com/FastTrackiverse/fasttrackpy'
+url: 'https://fasttrackiverse.github.io/fasttrackpy/'
+abstract: A python implementation of FastTrack
+license: MIT

README.md

@@ -1,6 +1,7 @@
 # FastTrackPy
 [![PyPI](https://img.shields.io/pypi/v/fasttrackpy)](https://pypi.org/project/fasttrackpy/)
-[![Python CI](https://github.com/JoFrhwld/fasttrackpy/actions/workflows/test-and-run.yml/badge.svg)](https://github.com/JoFrhwld/fasttrackpy/actions/workflows/test-and-run.yml) [![codecov](https://codecov.io/gh/FastTrackiverse/fasttrackpy/graph/badge.svg?token=GOAWY4B5C8)](https://codecov.io/gh/FastTrackiverse/fasttrackpy) <a href="https://codeclimate.com/github/JoFrhwld/fasttrackpy/maintainability"><img src="https://api.codeclimate.com/v1/badges/6725fded174b21a3c59f/maintainability" /></a>
+[![Python CI](https://github.com/JoFrhwld/fasttrackpy/actions/workflows/test-and-run.yml/badge.svg)](https://github.com/JoFrhwld/fasttrackpy/actions/workflows/test-and-run.yml) [![codecov](https://codecov.io/gh/FastTrackiverse/fasttrackpy/graph/badge.svg?token=GOAWY4B5C8)](https://codecov.io/gh/FastTrackiverse/fasttrackpy) <a href="https://codeclimate.com/github/JoFrhwld/fasttrackpy/maintainability"><img src="https://api.codeclimate.com/v1/badges/6725fded174b21a3c59f/maintainability" /></a> [![DOI](https://zenodo.org/badge/580169086.svg)](https://zenodo.org/doi/10.5281/zenodo.10212099)
+
 
 Goal: A FastTrack python implementation with importable modules
 
@@ -14,4 +15,4 @@ pip install fasttrackpy
 
 ```bash
 fasttrack --file audio.wav --output formants.csv
-```
+```

poetry.toml

@@ -0,0 +1,2 @@
+[virtualenvs]
+in-project = true

pyproject.toml

@@ -18,10 +18,10 @@ homepage = "https://fasttrackiverse.github.io/fasttrackpy/"
 repository = "https://github.com/FastTrackiverse/fasttrackpy"
 
 [tool.poetry.dependencies]
-python = ">=3.10,<3.13"
+python = ">=3.10,<3.12"
 praat-parselmouth = "^0.4.3"
-scipy = {version = "^1.11.3", python = ">=3.10,<3.13"}
-numpy = {version = "^1.26.1", python = ">=3.10,<3.13"}
+scipy = {version = "^1.11.3", python = ">=3.10,<3.12"}
+numpy = {version = "^1.26.1", python = ">=3.10,<3.12"}
 polars = "^0.19.16"
 pytest-cov = "^4.1.0"
 pytest = "^7.4.3"
@@ -59,7 +59,8 @@ addopts = [
     "--import-mode=importlib",
     "--cov-config=tests/.coveragerc",
     "--cov-report=xml",
-    "--cov"
+    "--cov",
+    "--log-cli-level=INFO"
 ]
 filterwarnings =[
     "ignore::UserWarning"

src/fasttrackpy/cli.py

@@ -251,7 +251,8 @@ def audio(
         n_formants: int = 4,
         window_length: float = 0.025,
         time_step: float = 0.002,
-        pre_emphasis_from: float = 50
+        pre_emphasis_from: float = 50,
+        **kwargs
 ):
     """Run fasttrack.
 
@@ -392,7 +393,8 @@ def audio_textgrid(
         n_formants: int = 4,
         window_length: float = 0.025,
         time_step: float = 0.002,
-        pre_emphasis_from: float = 50
+        pre_emphasis_from: float = 50,
+        **kwargs
 ):
     """Run fasttrack.
 

tests/test_cli.py

@@ -3,6 +3,7 @@
 from click.testing import CliRunner
 import pytest
 import yaml
+import logging
 
 class TestCLI:
     sound_path = Path("tests", "test_data", "ay.wav")
@@ -16,17 +17,21 @@ def test_file_usage(self):
             out_dir.mkdir()
 
         runner = CliRunner()
-        runner.invoke(
+        result = runner.invoke(
             fasttrack,
-            f"audio --file {str(self.sound_path)} --dest {str(out_dir)}"
+            ["audio", 
+             "--file", self.sound_path, 
+             "--dest", out_dir]
         )
+
+        assert result.exit_code == 0, result.output
         out_files = list(out_dir.glob("*"))
-        assert all([x.is_file() for x in out_files])
         [x.unlink() for x in out_files]
         out_dir.rmdir()
 
     def test_config_file(self):
-        with open("tests/test_data/config.yml") as file:
+        config_path = Path("tests", "test_data", "config.yml")
+        with config_path.open() as file:
             params = yaml.safe_load(file)
 
         sound_path = Path(params["file"])
@@ -35,12 +40,14 @@ def test_config_file(self):
             dest.mkdir()
 
         runner = CliRunner()
-        runner.invoke(
+        result = runner.invoke(
             fasttrack,
-            f"audio --config tests/test_data/config.yml"
+            ["audio", 
+             "--config", config_path]
         )
+
+        assert result.exit_code == 0, result.output
         out_files = list(dest.glob("*"))
-        assert all([x.is_file() for x in out_files])
         [x.unlink() for x in out_files]
         dest.rmdir()
 
@@ -51,14 +58,15 @@ def test_dir_usage(self):
             out_dir.mkdir()
 
         runner = CliRunner()
-        runner.invoke(
+        result = runner.invoke(
             fasttrack,
-            f"audio --dir {str(self.sound_path.parent)} --dest {str(out_dir)}"
+            ["audio", 
+             "--dir", self.sound_path.parent,
+               "--dest", out_dir]
         )
 
-        out_files = list(out_dir.glob("*"))
-        assert all([x.is_file() for x in out_files])
-
+        assert result.exit_code == 0, result.output
+        out_files = out_dir.glob("*")
         [x.unlink() for x in out_files]
         out_dir.rmdir()
 
@@ -67,13 +75,18 @@ def test_audio_tg(self):
         if not out_dir.is_dir():
             out_dir.mkdir()
         runner = CliRunner()
-        runner.invoke(
+        result = runner.invoke(
             fasttrack,
-            f"audio-textgrid --audio {str(self.audio_path)} --textgrid {str(self.tg_path)} --target-tier Phone --target-labels AY --dest {str(out_dir)}"
+            ["audio-textgrid", 
+             "--audio", self.audio_path, 
+             "--textgrid", self.tg_path, 
+             "--target-tier", "Phone", 
+             "--target-labels", "AY",
+             "--dest", out_dir]
         )
 
+        assert result.exit_code == 0, result.output
         out_files = list(out_dir.glob("*"))
-        assert all([x.is_file() for x in out_files])
 
         [x.unlink() for x in out_files]
         out_dir.rmdir()
@@ -83,14 +96,18 @@ def test_corpus(self):
         if not out_dir.is_dir():
             out_dir.mkdir()
         runner = CliRunner()
-        runner.invoke(
+        result = runner.invoke(
             fasttrack,
-            f"corpus --corpus {str(self.corpus_path)} --target-labels AY --dest {str(out_dir)} --separate-output"
+            ["corpus",
+             "--corpus", self.corpus_path,
+             "--target-labels", "AY",
+             "--dest", out_dir, 
+             "--separate-output"]
         )
 
+        assert result.exit_code == 0, result.output
         out_files = list(out_dir.iterdir())
-        assert all([x.is_file() for x in out_files])
-        #assert len(out_files) > 1
+        assert len(out_files) > 1
 
         [x.unlink() for x in out_files]
         out_dir.rmdir()