Prep 2.0.3 release

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,40 @@
+name: Bug Report
+description: The software does something unwanted or unusual
+title: "[BUG]: "
+labels: ["bug"]
+
+body:
+  - type: markdown
+    attributes: 
+      value: |
+        Thanks for taking the time to fill out this bug report!
+  - type: checkboxes
+    id: new-bug
+    attributes:
+      label: Did you search for similar bugs?
+      description: Please search to see if an issue already exists for the bug you encountered.
+      options:
+      - label: I have searched the existing issues
+        required: false
+  - type: textarea
+    id: bug-description
+    attributes:
+      label: What happened?
+      description: Tell us what bug you encountered
+    validations:
+      required: true
+  - type: textarea
+    id: bug-behaviour
+    attributes:
+      label: Expectations?
+      description: Tell us what should have happened
+    validations:
+      required: true
+  - type: textarea
+    id: steps-to-reproduce
+    attributes:
+      label: Steps To Reproduce
+      description: Can you describe your steps, when you encountered the bug?
+      placeholder: Please write the steps in a list form
+    validations:
+      required: false

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

@@ -19,20 +19,24 @@ jobs:
     runs-on: ${{ matrix.os }}
     steps:
     - uses: actions/checkout@v3
+    - name: Install poetry
+      run: pipx install poetry
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
+        cache: 'poetry'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest
+        poetry env use "${{ matrix.python-version }}"
+        poetry install
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        poetry run flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        poetry run flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
-        python -m pytest tests/
+        poetry run pytest tests/

.gitignore

@@ -7,6 +7,7 @@
 *.wav
 build/*
 docs/_build
+*.code-workspace
 *.swp
 *.orig
 env

README.md

@@ -34,10 +34,16 @@ You can find user support for installing and using the FAVE toolkits at the [FAV
 ## Contributing to FAVE
 For the most part, we'll be utilizing the fork-and-pull paradigm (see [Using Pull Requests](https://help.github.com/articles/using-pull-requests)). Please send pull requests to the `dev` branch.
 
-If you want to keep up to date on FAVE development, or have questions about FAVE development, send a request to join the [FAVE Developers' Group](https://groups.google.com/forum/#!forum/fave-dev).
+You can fill in a bug report at the [issue tab](https://github.com/JoFrhwld/FAVE/issues)
+
+There may be a delay between when a bug is reported and when a bug is resolved. Developers prioritize bugs based on difficulty, importance, and other factors, so bug reports are usually not handled in the order they are received. 
 
 ## Attribution
-[![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.22281.svg)](http://dx.doi.org/10.5281/zenodo.22281)
+[![DOI](https://zenodo.org/badge/13744621.svg)](https://zenodo.org/badge/latestdoi/13744621)
+![GitHub](https://img.shields.io/github/license/JoFrhwld/FAVE)
+![GitHub](https://img.shields.io/badge/Python-3.8%2B-brightgreen)
+[![PyPI version fury.io](https://badge.fury.io/py/fave.svg)](https://pypi.python.org/pypi/fave/)
+
 As of v1.1.3 onwards, releases from this repository will have a DOI associated with them through Zenodo. The DOI for the current release is [10.5281/zenodo.22281](http://dx.doi.org/10.5281/zenodo.22281). We would recommend the citation:
 
 Rosenfelder, Ingrid; Fruehwald, Josef; Brickhouse, Christian; Evanini, Keelan; Seyfarth, Scott; Gorman, Kyle; Prichard, Hilary; Yuan, Jiahong; 2022. FAVE (Forced Alignment and Vowel Extraction) Program Suite v2.0.0 */zenodo.*

docs/_build/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 95450042ea89bddbb1481c62b8e92e75
+config: a9e501948c645bf032c7e86e32c92cb5
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/_build/html/_sources/index.rst.txt

@@ -6,21 +6,21 @@
 Forced Alignment and Vowel Extraction (FAVE)
 ============================================
 
-Welcome to the FAVE documentation
+This website documents the FAVE software, version 2. 
 
+.. warning::
+   If you have used FAVE before, please read :doc:`usage/whats-new` to familiarize yourself with the differences between the current and legacy versions of FAVE. 
+
+Guides and documentation
+------------------------
 .. toctree::
    :maxdepth: 2
 
-   Installing FAVE <usage/installation>
-   Quickstart guide <usage/quickstart>
-   fave.align module <code/align/index>
-   fave.extract module <code/extract/index>
-   code/cmudictionary
-   code/praat
-
+   usage/index
+   code/index
 
-Indices and tables
-==================
+Indices
+-------
 
 * :ref:`genindex`
 * :ref:`modindex`

docs/_build/html/_sources/usage/installation.rst.txt

@@ -1,4 +1,27 @@
-Installing FAVE 2.0
-===================
+Installing FAVE 2
+=================
 
-To be created
+Required software
+-----------------
+
+FAVE sometimes requires other software libraries in order to work. 
+ * FAVE-align requires `SoX <http://sox.sourceforge.net/>`_ and `HTK <https://htk.eng.cam.ac.uk/>`_.
+ * FAVE-extract requires `Praat <https://www.fon.hum.uva.nl/praat/>`_.
+
+You will need to manually install these if they are not already installed on your computer.
+
+.. warning::
+   Mac users: HTK might need slight modification before it works. See `this bug report <https://github.com/JoFrhwld/FAVE/issues/48>`_.
+
+Install with PIP
+----------------
+
+FAVE is available on the Python Package Index (PyPI) as ``fave``. You can install it using:
+
+.. code-block:: console
+
+   python3 -m pip install fave
+
+Other package managers
+^^^^^^^^^^^^^^^^^^^^^^
+Work is ongoing to publish FAVE as a debian package, but no other package system is supported at the moment. If you would like to package FAVE for your system, please feel free to :doc:`contribute <../contributing>`!

docs/_build/html/_sources/usage/quickstart.rst.txt

@@ -1,4 +1,24 @@
 Quickstart guide to using FAVE 2.0
 ==================================
 
-To be created
+ #. Install FAVE and its dependencies according to :doc:`the directions <installation>`.
+ #. Download the ``FAAValign.py`` and ``extractFormants.py`` scripts.
+ #. Check your transcription for out-of-dictionary words
+
+    .. code-block:: console
+       :caption: Check for out-of-dictionary words
+
+       python3 FAAValign.py --check unknown_words.txt AudioFile.wav TranscriptionFile.txt OutputAlignment.TextGrid
+ #. Open ``unknown_words.txt`` and create a transcription for each word listed.
+ #. Align your audio and transcripts including your new transcriptions:
+
+    .. code-block:: console
+       :caption: Begin forced alignment
+
+       python3 FAAValign.py --import custom_dictionary.txt AudioFile.wav TranscriptionFile.txt OutputAlignment.TextGrid
+ #. Extract formant data using the default settings:
+
+    .. code-block:: console
+       :caption: Extract formant data
+
+       python3 extractFormants.py AudioFile.wav Alignment.TextGrid OutputFileName.tsv