diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 19d47a6..1ce4481 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -13,24 +13,26 @@ jobs: steps: - uses: actions/checkout@v4 + + # Following steps given here: https://docs.astral.sh/uv/guides/integration/github/#setting-up-python + - name: Install uv + uses: astral-sh/setup-uv@v3 + - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 - with: - python-version: ${{ matrix.python-version }} - - name: Install dependencies - run: | - python -m pip install --upgrade pip - if [ -f requirements.lock ]; then pip install -r requirements.lock; fi + run: uv python install ${{ matrix.python-version }} + + - name: Install the project + run: uv sync --all-extras --dev + - name: Lint with Ruff - run: | - pip install ruff - ruff --format=github --target-version=py310 . + run: uv run ruff check --output-format=github --target-version=py310 . continue-on-error: true + - name: Test with pytest run: | - pip install coverage pytest - coverage run -m pytest -v -s + uv pip install pytest-cov + uv run pytest -v -s --cov=acoustic_toolbox tests/ + - name: Generate Coverage Report - run: | - coverage report -m + run: uv run coverage report -m \ No newline at end of file diff --git a/.readthedocs.yaml b/.readthedocs.yaml index dafb1d5..4e3793e 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -3,16 +3,16 @@ version: "2" build: os: "ubuntu-22.04" tools: - python: "3.10" + python: "3.12" apt_packages: - graphviz - -python: - install: - - requirements: docs/requirements.txt - # Install our python package before building the docs - - method: pip - path: . + commands: +# Following documentation at https://docs.readthedocs.io/en/latest/build-customization.html#install-dependencies-with-uv + - asdf plugin add uv + - asdf install uv latest + - asdf global uv latest + - uv sync --extra docs --frozen + - uv run -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html sphinx: configuration: docs/source/conf.py diff --git a/README.md b/README.md index 7a01c4d..a115dbd 100644 --- a/README.md +++ b/README.md @@ -26,7 +26,7 @@ Several examples can be found in the `examples` folder. The test suite can be run with -`pytest` +`uv run pytest` ## Documentation @@ -40,6 +40,11 @@ Documentation can be found [online](http://acoustic-toolbox.readthedocs.io/). Contributors are always welcome. +Setting up the development environment and dependency management is done with `uv`. `uv` can be installed [from source](https://docs.astral.sh/uv/getting-started/installation/#standalone-installer) or with `pip install uv`. + +To install the development environment, run `uv sync --all-extras` in the root of the repository. This will setup a `.venv` and install all dependencies including dev and docs dependencies. + +Documentation is built with `uv run make html` from the `docs` folder and can be viewed in the `docs/build/html` folder. ## Origin project diff --git a/pyproject.toml b/pyproject.toml index f01bc87..f655f0e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -45,10 +45,12 @@ docs = [ [tool.flit.sdist] include = ["tests/"] -[tool.rye] -universal = true +[tool.uv] dev-dependencies = [ "ruff>=0.5.5", "pytest>=8.3.2", "coverage>=7.6.0", ] + +[tool.uv.pip] +universal = true diff --git a/requirements-dev.lock b/requirements-dev.lock deleted file mode 100644 index d977247..0000000 --- a/requirements-dev.lock +++ /dev/null @@ -1,396 +0,0 @@ -# generated by rye -# use `rye lock` or `rye sync` to update this lockfile -# -# last locked with the following flags: -# pre: false -# features: [] -# all-features: true -# with-sources: false - --e file:. -alabaster==0.7.16 - # via sphinx -anyio==4.4.0 - # via httpx - # via jupyter-server -appnope==0.1.4 - # via ipykernel -argon2-cffi==23.1.0 - # via jupyter-server -argon2-cffi-bindings==21.2.0 - # via argon2-cffi -arrow==1.3.0 - # via isoduration -asttokens==2.4.1 - # via stack-data -async-lru==2.0.4 - # via jupyterlab -attrs==23.2.0 - # via jsonschema - # via referencing -babel==2.15.0 - # via jupyterlab-server - # via sphinx -beautifulsoup4==4.12.3 - # via nbconvert -bleach==6.1.0 - # via nbconvert -certifi==2024.7.4 - # via httpcore - # via httpx - # via requests -cffi==1.16.0 - # via argon2-cffi-bindings - # via pysoundfile -charset-normalizer==3.3.2 - # via requests -comm==0.2.2 - # via ipykernel - # via ipywidgets -contourpy==1.2.1 - # via matplotlib -coverage==7.6.0 -cycler==0.12.1 - # via matplotlib -debugpy==1.8.2 - # via ipykernel -decorator==5.1.1 - # via ipython -defusedxml==0.7.1 - # via nbconvert -docutils==0.18.1 - # via nbsphinx - # via sphinx - # via sphinx-rtd-theme -exceptiongroup==1.2.2 - # via anyio - # via ipython - # via pytest -executing==2.0.1 - # via stack-data -fastjsonschema==2.20.0 - # via nbformat -fonttools==4.53.1 - # via matplotlib -fqdn==1.5.1 - # via jsonschema -h11==0.14.0 - # via httpcore -httpcore==1.0.5 - # via httpx -httpx==0.27.0 - # via jupyterlab -idna==3.7 - # via anyio - # via httpx - # via jsonschema - # via requests -imagesize==1.4.1 - # via sphinx -iniconfig==2.0.0 - # via pytest -ipykernel==6.29.5 - # via jupyter - # via jupyter-console - # via jupyterlab - # via qtconsole -ipython==8.26.0 - # via ipykernel - # via ipywidgets - # via jupyter-console -ipywidgets==8.1.3 - # via jupyter -isoduration==20.11.0 - # via jsonschema -jedi==0.19.1 - # via ipython -jinja2==3.1.4 - # via jupyter-server - # via jupyterlab - # via jupyterlab-server - # via nbconvert - # via nbsphinx - # via sphinx -json5==0.9.25 - # via jupyterlab-server -jsonpointer==3.0.0 - # via jsonschema -jsonschema==4.23.0 - # via jupyter-events - # via jupyterlab-server - # via nbformat -jsonschema-specifications==2023.12.1 - # via jsonschema -jupyter==1.0.0 - # via acoustic-toolbox -jupyter-client==8.6.2 - # via ipykernel - # via jupyter-console - # via jupyter-server - # via nbclient - # via qtconsole -jupyter-console==6.6.3 - # via jupyter -jupyter-core==5.7.2 - # via ipykernel - # via jupyter-client - # via jupyter-console - # via jupyter-server - # via jupyterlab - # via nbclient - # via nbconvert - # via nbformat - # via qtconsole -jupyter-events==0.10.0 - # via jupyter-server -jupyter-lsp==2.2.5 - # via jupyterlab -jupyter-server==2.14.2 - # via jupyter-lsp - # via jupyterlab - # via jupyterlab-server - # via notebook - # via notebook-shim -jupyter-server-terminals==0.5.3 - # via jupyter-server -jupyterlab==4.2.4 - # via notebook -jupyterlab-pygments==0.3.0 - # via nbconvert -jupyterlab-server==2.27.3 - # via jupyterlab - # via notebook -jupyterlab-widgets==3.0.11 - # via ipywidgets -kiwisolver==1.4.5 - # via matplotlib -markupsafe==2.1.5 - # via jinja2 - # via nbconvert -matplotlib==3.9.1 - # via acoustic-toolbox -matplotlib-inline==0.1.7 - # via ipykernel - # via ipython -mistune==3.0.2 - # via nbconvert -nbclient==0.10.0 - # via nbconvert -nbconvert==7.16.4 - # via jupyter - # via jupyter-server - # via nbsphinx -nbformat==5.10.4 - # via jupyter-server - # via nbclient - # via nbconvert - # via nbsphinx -nbsphinx==0.9.4 - # via acoustic-toolbox - # via nbsphinx-link -nbsphinx-link==1.3.0 - # via acoustic-toolbox -nest-asyncio==1.6.0 - # via ipykernel -notebook==7.2.1 - # via jupyter -notebook-shim==0.2.4 - # via jupyterlab - # via notebook -numpy==2.0.1 - # via acoustic-toolbox - # via contourpy - # via matplotlib - # via pandas - # via scipy -overrides==7.7.0 - # via jupyter-server -packaging==24.1 - # via ipykernel - # via jupyter-server - # via jupyterlab - # via jupyterlab-server - # via matplotlib - # via nbconvert - # via pytest - # via qtconsole - # via qtpy - # via sphinx -pandas==2.2.2 - # via acoustic-toolbox -pandocfilters==1.5.1 - # via nbconvert -parso==0.8.4 - # via jedi -pexpect==4.9.0 - # via ipython -pillow==10.4.0 - # via matplotlib -platformdirs==4.2.2 - # via jupyter-core -pluggy==1.5.0 - # via pytest -prometheus-client==0.20.0 - # via jupyter-server -prompt-toolkit==3.0.47 - # via ipython - # via jupyter-console -psutil==6.0.0 - # via ipykernel -ptyprocess==0.7.0 - # via pexpect - # via terminado -pure-eval==0.2.3 - # via stack-data -pycparser==2.22 - # via cffi -pygments==2.18.0 - # via ipython - # via jupyter-console - # via nbconvert - # via qtconsole - # via sphinx -pyparsing==3.1.2 - # via matplotlib -pysoundfile==0.9.0.post1 - # via acoustic-toolbox -pytest==8.3.2 -python-dateutil==2.9.0.post0 - # via arrow - # via jupyter-client - # via matplotlib - # via pandas -python-json-logger==2.0.7 - # via jupyter-events -pytz==2024.1 - # via pandas -pyyaml==6.0.1 - # via jupyter-events -pyzmq==26.0.3 - # via ipykernel - # via jupyter-client - # via jupyter-console - # via jupyter-server - # via qtconsole -qtconsole==5.5.2 - # via jupyter -qtpy==2.4.1 - # via qtconsole -referencing==0.35.1 - # via jsonschema - # via jsonschema-specifications - # via jupyter-events -requests==2.32.3 - # via jupyterlab-server - # via sphinx -rfc3339-validator==0.1.4 - # via jsonschema - # via jupyter-events -rfc3986-validator==0.1.1 - # via jsonschema - # via jupyter-events -rpds-py==0.19.1 - # via jsonschema - # via referencing -ruff==0.5.5 -scipy==1.14.0 - # via acoustic-toolbox -send2trash==1.8.3 - # via jupyter-server -setuptools==72.1.0 - # via jupyterlab -six==1.16.0 - # via acoustic-toolbox - # via asttokens - # via bleach - # via python-dateutil - # via rfc3339-validator -sniffio==1.3.1 - # via anyio - # via httpx -snowballstemmer==2.2.0 - # via sphinx -soupsieve==2.5 - # via beautifulsoup4 -sphinx==7.3.7 - # via acoustic-toolbox - # via nbsphinx - # via nbsphinx-link - # via sphinx-rtd-theme - # via sphinxcontrib-jquery -sphinx-rtd-theme==1.3.0rc1 - # via acoustic-toolbox -sphinxcontrib-applehelp==2.0.0 - # via sphinx -sphinxcontrib-devhelp==2.0.0 - # via sphinx -sphinxcontrib-htmlhelp==2.1.0 - # via sphinx -sphinxcontrib-jquery==4.1 - # via sphinx-rtd-theme -sphinxcontrib-jsmath==1.0.1 - # via sphinx -sphinxcontrib-qthelp==2.0.0 - # via sphinx -sphinxcontrib-serializinghtml==2.0.0 - # via sphinx -stack-data==0.6.3 - # via ipython -tabulate==0.9.0 - # via acoustic-toolbox -terminado==0.18.1 - # via jupyter-server - # via jupyter-server-terminals -tinycss2==1.3.0 - # via nbconvert -tomli==2.0.1 - # via jupyterlab - # via pytest - # via sphinx -tornado==6.4.1 - # via ipykernel - # via jupyter-client - # via jupyter-server - # via jupyterlab - # via notebook - # via terminado -traitlets==5.14.3 - # via comm - # via ipykernel - # via ipython - # via ipywidgets - # via jupyter-client - # via jupyter-console - # via jupyter-core - # via jupyter-events - # via jupyter-server - # via jupyterlab - # via matplotlib-inline - # via nbclient - # via nbconvert - # via nbformat - # via nbsphinx - # via qtconsole -types-python-dateutil==2.9.0.20240316 - # via arrow -typing-extensions==4.12.2 - # via anyio - # via async-lru - # via ipython -tzdata==2024.1 - # via pandas -uri-template==1.3.0 - # via jsonschema -urllib3==2.2.2 - # via requests -wcwidth==0.2.13 - # via prompt-toolkit -webcolors==24.6.0 - # via jsonschema -webencodings==0.5.1 - # via bleach - # via tinycss2 -websocket-client==1.8.0 - # via jupyter-server -widgetsnbextension==4.0.11 - # via ipywidgets diff --git a/requirements.lock b/requirements.lock deleted file mode 100644 index 8325dae..0000000 --- a/requirements.lock +++ /dev/null @@ -1,386 +0,0 @@ -# generated by rye -# use `rye lock` or `rye sync` to update this lockfile -# -# last locked with the following flags: -# pre: false -# features: [] -# all-features: true -# with-sources: false - --e file:. -alabaster==0.7.16 - # via sphinx -anyio==4.4.0 - # via httpx - # via jupyter-server -appnope==0.1.4 - # via ipykernel -argon2-cffi==23.1.0 - # via jupyter-server -argon2-cffi-bindings==21.2.0 - # via argon2-cffi -arrow==1.3.0 - # via isoduration -asttokens==2.4.1 - # via stack-data -async-lru==2.0.4 - # via jupyterlab -attrs==23.2.0 - # via jsonschema - # via referencing -babel==2.15.0 - # via jupyterlab-server - # via sphinx -beautifulsoup4==4.12.3 - # via nbconvert -bleach==6.1.0 - # via nbconvert -certifi==2024.7.4 - # via httpcore - # via httpx - # via requests -cffi==1.16.0 - # via argon2-cffi-bindings - # via pysoundfile -charset-normalizer==3.3.2 - # via requests -comm==0.2.2 - # via ipykernel - # via ipywidgets -contourpy==1.2.1 - # via matplotlib -cycler==0.12.1 - # via matplotlib -debugpy==1.8.2 - # via ipykernel -decorator==5.1.1 - # via ipython -defusedxml==0.7.1 - # via nbconvert -docutils==0.18.1 - # via nbsphinx - # via sphinx - # via sphinx-rtd-theme -exceptiongroup==1.2.2 - # via anyio - # via ipython -executing==2.0.1 - # via stack-data -fastjsonschema==2.20.0 - # via nbformat -fonttools==4.53.1 - # via matplotlib -fqdn==1.5.1 - # via jsonschema -h11==0.14.0 - # via httpcore -httpcore==1.0.5 - # via httpx -httpx==0.27.0 - # via jupyterlab -idna==3.7 - # via anyio - # via httpx - # via jsonschema - # via requests -imagesize==1.4.1 - # via sphinx -ipykernel==6.29.5 - # via jupyter - # via jupyter-console - # via jupyterlab - # via qtconsole -ipython==8.26.0 - # via ipykernel - # via ipywidgets - # via jupyter-console -ipywidgets==8.1.3 - # via jupyter -isoduration==20.11.0 - # via jsonschema -jedi==0.19.1 - # via ipython -jinja2==3.1.4 - # via jupyter-server - # via jupyterlab - # via jupyterlab-server - # via nbconvert - # via nbsphinx - # via sphinx -json5==0.9.25 - # via jupyterlab-server -jsonpointer==3.0.0 - # via jsonschema -jsonschema==4.23.0 - # via jupyter-events - # via jupyterlab-server - # via nbformat -jsonschema-specifications==2023.12.1 - # via jsonschema -jupyter==1.0.0 - # via acoustic-toolbox -jupyter-client==8.6.2 - # via ipykernel - # via jupyter-console - # via jupyter-server - # via nbclient - # via qtconsole -jupyter-console==6.6.3 - # via jupyter -jupyter-core==5.7.2 - # via ipykernel - # via jupyter-client - # via jupyter-console - # via jupyter-server - # via jupyterlab - # via nbclient - # via nbconvert - # via nbformat - # via qtconsole -jupyter-events==0.10.0 - # via jupyter-server -jupyter-lsp==2.2.5 - # via jupyterlab -jupyter-server==2.14.2 - # via jupyter-lsp - # via jupyterlab - # via jupyterlab-server - # via notebook - # via notebook-shim -jupyter-server-terminals==0.5.3 - # via jupyter-server -jupyterlab==4.2.4 - # via notebook -jupyterlab-pygments==0.3.0 - # via nbconvert -jupyterlab-server==2.27.3 - # via jupyterlab - # via notebook -jupyterlab-widgets==3.0.11 - # via ipywidgets -kiwisolver==1.4.5 - # via matplotlib -markupsafe==2.1.5 - # via jinja2 - # via nbconvert -matplotlib==3.9.1 - # via acoustic-toolbox -matplotlib-inline==0.1.7 - # via ipykernel - # via ipython -mistune==3.0.2 - # via nbconvert -nbclient==0.10.0 - # via nbconvert -nbconvert==7.16.4 - # via jupyter - # via jupyter-server - # via nbsphinx -nbformat==5.10.4 - # via jupyter-server - # via nbclient - # via nbconvert - # via nbsphinx -nbsphinx==0.9.4 - # via acoustic-toolbox - # via nbsphinx-link -nbsphinx-link==1.3.0 - # via acoustic-toolbox -nest-asyncio==1.6.0 - # via ipykernel -notebook==7.2.1 - # via jupyter -notebook-shim==0.2.4 - # via jupyterlab - # via notebook -numpy==2.0.1 - # via acoustic-toolbox - # via contourpy - # via matplotlib - # via pandas - # via scipy -overrides==7.7.0 - # via jupyter-server -packaging==24.1 - # via ipykernel - # via jupyter-server - # via jupyterlab - # via jupyterlab-server - # via matplotlib - # via nbconvert - # via qtconsole - # via qtpy - # via sphinx -pandas==2.2.2 - # via acoustic-toolbox -pandocfilters==1.5.1 - # via nbconvert -parso==0.8.4 - # via jedi -pexpect==4.9.0 - # via ipython -pillow==10.4.0 - # via matplotlib -platformdirs==4.2.2 - # via jupyter-core -prometheus-client==0.20.0 - # via jupyter-server -prompt-toolkit==3.0.47 - # via ipython - # via jupyter-console -psutil==6.0.0 - # via ipykernel -ptyprocess==0.7.0 - # via pexpect - # via terminado -pure-eval==0.2.3 - # via stack-data -pycparser==2.22 - # via cffi -pygments==2.18.0 - # via ipython - # via jupyter-console - # via nbconvert - # via qtconsole - # via sphinx -pyparsing==3.1.2 - # via matplotlib -pysoundfile==0.9.0.post1 - # via acoustic-toolbox -python-dateutil==2.9.0.post0 - # via arrow - # via jupyter-client - # via matplotlib - # via pandas -python-json-logger==2.0.7 - # via jupyter-events -pytz==2024.1 - # via pandas -pyyaml==6.0.1 - # via jupyter-events -pyzmq==26.0.3 - # via ipykernel - # via jupyter-client - # via jupyter-console - # via jupyter-server - # via qtconsole -qtconsole==5.5.2 - # via jupyter -qtpy==2.4.1 - # via qtconsole -referencing==0.35.1 - # via jsonschema - # via jsonschema-specifications - # via jupyter-events -requests==2.32.3 - # via jupyterlab-server - # via sphinx -rfc3339-validator==0.1.4 - # via jsonschema - # via jupyter-events -rfc3986-validator==0.1.1 - # via jsonschema - # via jupyter-events -rpds-py==0.19.1 - # via jsonschema - # via referencing -scipy==1.14.0 - # via acoustic-toolbox -send2trash==1.8.3 - # via jupyter-server -setuptools==72.1.0 - # via jupyterlab -six==1.16.0 - # via acoustic-toolbox - # via asttokens - # via bleach - # via python-dateutil - # via rfc3339-validator -sniffio==1.3.1 - # via anyio - # via httpx -snowballstemmer==2.2.0 - # via sphinx -soupsieve==2.5 - # via beautifulsoup4 -sphinx==7.3.7 - # via acoustic-toolbox - # via nbsphinx - # via nbsphinx-link - # via sphinx-rtd-theme - # via sphinxcontrib-jquery -sphinx-rtd-theme==1.3.0rc1 - # via acoustic-toolbox -sphinxcontrib-applehelp==2.0.0 - # via sphinx -sphinxcontrib-devhelp==2.0.0 - # via sphinx -sphinxcontrib-htmlhelp==2.1.0 - # via sphinx -sphinxcontrib-jquery==4.1 - # via sphinx-rtd-theme -sphinxcontrib-jsmath==1.0.1 - # via sphinx -sphinxcontrib-qthelp==2.0.0 - # via sphinx -sphinxcontrib-serializinghtml==2.0.0 - # via sphinx -stack-data==0.6.3 - # via ipython -tabulate==0.9.0 - # via acoustic-toolbox -terminado==0.18.1 - # via jupyter-server - # via jupyter-server-terminals -tinycss2==1.3.0 - # via nbconvert -tomli==2.0.1 - # via jupyterlab - # via sphinx -tornado==6.4.1 - # via ipykernel - # via jupyter-client - # via jupyter-server - # via jupyterlab - # via notebook - # via terminado -traitlets==5.14.3 - # via comm - # via ipykernel - # via ipython - # via ipywidgets - # via jupyter-client - # via jupyter-console - # via jupyter-core - # via jupyter-events - # via jupyter-server - # via jupyterlab - # via matplotlib-inline - # via nbclient - # via nbconvert - # via nbformat - # via nbsphinx - # via qtconsole -types-python-dateutil==2.9.0.20240316 - # via arrow -typing-extensions==4.12.2 - # via anyio - # via async-lru - # via ipython -tzdata==2024.1 - # via pandas -uri-template==1.3.0 - # via jsonschema -urllib3==2.2.2 - # via requests -wcwidth==0.2.13 - # via prompt-toolkit -webcolors==24.6.0 - # via jsonschema -webencodings==0.5.1 - # via bleach - # via tinycss2 -websocket-client==1.8.0 - # via jupyter-server -widgetsnbextension==4.0.11 - # via ipywidgets diff --git a/uv.lock b/uv.lock new file mode 100644 index 0000000..9d5dab7 --- /dev/null +++ b/uv.lock @@ -0,0 +1,2426 @@ +version = 1 +requires-python = ">=3.10" +resolution-markers = [ + "python_full_version < '3.11'", + "python_full_version == '3.11.*'", + "python_full_version >= '3.12'", +] + +[[package]] +name = "acoustic-toolbox" +version = "0.1.1" +source = { editable = "." } +dependencies = [ + { name = "matplotlib" }, + { name = "numpy" }, + { name = "pandas" }, + { name = "pysoundfile" }, + { name = "scipy" }, + { name = "six" }, + { name = "tabulate" }, +] + +[package.optional-dependencies] +docs = [ + { name = "jupyter" }, + { name = "nbsphinx" }, + { name = "nbsphinx-link" }, + { name = "sphinx" }, + { name 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