Merge pull request #557 from kitzeslab/develop

v0.7.1

Author: sammlapp

.github/workflows/poetry.yml

@@ -23,10 +23,10 @@ jobs:
       - name: Install ffmpeg v4
         run: sudo snap install ffmpeg
       - name: Install poetry
-        run: curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python
+        run: curl -sSL https://install.python-poetry.org | python
       - name: Poetry install
-        run: ~/.poetry/bin/poetry install
+        run: /home/runner/.local/bin/poetry install
       - name: Poetry run pytest
-        run: ~/.poetry/bin/poetry run pytest
+        run: /home/runner/.local/bin/poetry run pytest
       - name: Poetry run black check
-        run: ~/.poetry/bin/poetry run black . --check --diff
+        run: /home/runner/.local/bin/poetry run black . --check --diff

.gitignore

@@ -7,3 +7,4 @@ doc/_build/
 *.ipynb_checkpoints/
 *.DS_Store
 docs/tutorials/woodcock_labeled_data
+.vscode

.pre-commit-config.yaml

@@ -1,5 +1,10 @@
 repos:
--   repo: https://github.com/psf/black
-    rev: 19.3b0
+  - repo: https://github.com/psf/black
+    rev: 22.8.0
     hooks:
-    - id: black
+      - id: black
+        # It is recommended to specify the latest version of Python
+        # supported by your project here, or alternatively use
+        # pre-commit's default_language_version, see
+        # https://pre-commit.com/#top_level-default_language_version
+        # language_version: python3.9

README.md

@@ -12,14 +12,14 @@ OpenSoundscape is currently in active development. If you find a bug, please sub
 
 #### Suggested Citation
 ```
-Lapp, Rhinehart, Freeland-Haynes, Khilnani, and Kitzes, 2022. "OpenSoundscape v0.7.0".
+Lapp, Rhinehart, Freeland-Haynes, Khilnani, Syunkova, and Kitzes, 2022. "OpenSoundscape v0.7.1".
 ```
 
 # Installation
 
-OpenSoundscape can be installed on Windows, Mac, and Linux machines. It has been tested on Python 3.7 and 3.8.
+OpenSoundscape can be installed on Windows, Mac, and Linux machines. It has been tested on Python 3.7 and 3.8. However, for Apple Silicon (M1 chip) users, Python 3.9 is recommended and may be required to avoid dependency issues. 
 
-Most users should install OpenSoundscape via pip: `pip install opensoundscape==0.7.0`. Contributors and advanced users can also use Poetry to install OpenSoundscape.
+Most users should install OpenSoundscape via pip: `pip install opensoundscape==0.7.1`. Contributors and advanced users can also use Poetry to install OpenSoundscape.
 
 For more detailed instructions on how to install OpenSoundscape and use it in Jupyter, see the [documentation](http://opensoundscape.org).
 

docs/api/modules.rst

@@ -60,6 +60,12 @@ Data Selection
 .. automodule:: opensoundscape.data_selection
   :members:
 
+Datasets
+^^^^^^^^
+
+.. automodule:: opensoundscape.torch.datasets
+  :members:
+
 
 Grad Cam
 ^^^^^^^^

docs/conf.py

@@ -22,11 +22,11 @@
 # -- Project information -----------------------------------------------------
 
 project = "opensoundscape"
-copyright = "2022 Sam Lapp, Tessa Rhinehart, Louis Freeland-Haynes, Justin Kitzes"
-author = "Sam Lapp, Tessa Rhinehart, Louis Freeland-Haynes, Justin Kitzes"
+copyright = "2022 Sam Lapp, Tessa Rhinehart, Louis Freeland-Haynes, Jatin Khilnani, Alexandra Syunkova, Justin Kitzes"
+author = "Sam Lapp, Tessa Rhinehart, Louis Freeland-Haynes, Jatin Khilnani, Alexandra Syunkova, Justin Kitzes"
 
 # The full version, including alpha/beta/rc tags
-release = "0.7.0"
+release = "0.7.1"
 
 
 # -- General configuration ---------------------------------------------------

docs/installation/mac_and_linux.md

@@ -1,6 +1,6 @@
 # Mac and Linux
 
-OpenSoundscape can be installed on Mac and Linux machines with Python 3.7 (or 3.8) using the pip command `pip install opensoundscape==0.7.0`. We recommend installing OpenSoundscape in a virtual environment to prevent dependency conflicts.
+OpenSoundscape can be installed on Mac and Linux machines with Python 3.7 (or 3.8) using the pip command `pip install opensoundscape==0.7.1`. We recommend installing OpenSoundscape in a virtual environment to prevent dependency conflicts.
 
 Below are instructions for installation with two package managers:
 * `conda`: Python and package management through Anaconda, a package manager popular among scientific programmers
@@ -15,7 +15,7 @@ Feel free to use another virtual environment manager (e.g. `virtualenvwrapper`)
    * follow the [installation instructions](https://docs.anaconda.com/anaconda/install/) for your operating system.
 * Create a Python 3.7 (or 3.8) conda environment for opensoundscape: `conda create --name opensoundscape pip python=3.7`
 * Activate the environment: `conda activate opensoundscape`
-* Install opensoundscape using pip: `pip install opensoundscape==0.7.0`
+* Install opensoundscape using pip: `pip install opensoundscape==0.7.1`
 * Deactivate the environment when you're done using it: `conda deactivate`
 
 ## Installation via `venv`
@@ -29,7 +29,7 @@ Run the following commands in your bash terminal:
 * Make a directory for virtual environments and `cd` into it: `mkdir .venv && cd .venv`
 * Create an environment called `opensoundscape` in the directory: `python3 -m venv opensoundscape`
 * Activate/use the environment: `source opensoundscape/bin/activate`
-* Install OpenSoundscape in the environment: `pip install opensoundscape==0.7.0`
+* Install OpenSoundscape in the environment: `pip install opensoundscape==0.7.1`
 * Once you are done with OpenSoundscape, deactivate the environment: `deactivate`
 * To use the environment again, you will have to refer to absolute path of the virtual environments folder. For instance, if I were on a Mac and created `.venv` inside a directory `/Users/MyFiles/Code` I would activate the virtual environment using: `source /Users/MyFiles/Code/.venv/opensoundscape/bin/activate`
 

docs/installation/windows.md

@@ -51,7 +51,7 @@ You can now manage packages with `conda`.
 ## Install OpenSoundscape in virtual environment
 - Create a Python 3.7 (or 3.8) conda environment for opensoundscape: `conda create --name opensoundscape pip python=3.7`
 - Activate the environment: `conda activate opensoundscape`
-- Install opensoundscape using pip: `pip install opensoundscape==0.7.0`
+- Install opensoundscape using pip: `pip install opensoundscape==0.7.1`
 
 If you see an error that says "No matching distribution found...", your
 best bet is to use these commands to download then install the package:
@@ -64,7 +64,7 @@ pip install .
 
 If you run into this error and you are on a Windows 10 machine:
 ```
-(opensoundscape_environment) username@computername:~$ pip install opensoundscape==0.7.0
+(opensoundscape_environment) username@computername:~$ pip install opensoundscape==0.7.1
 WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7f7603c5da90>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/opensoundscape/
 ```
 You may be able to solve it by going to System Settings, searching for “Proxy Settings,” and beneath “Automatic proxy setup,” turning “Automatically detect settings” OFF. Restart your terminal for changes to take effect. Then activate the environment and install OpenSoundscape using pip.

docs/requirements.txt

@@ -3,3 +3,4 @@ ipykernel
 nbsphinx
 m2r
 docutils<0.18
+mistune<2.0.0