Repository: Universite-Gustave-Eiffel/acoustic-toolbox (language: python)

Issue:
Use Rye for package dependencies
Looks good i'll switch to that !

From what I've red we need to remove requirements.txt and rely on pyproject.toml for dependencies.
I believe `requirements(-dev).lock` files should be committed though



Discussion / hints:
@Nitnelav I know we just changed to Rye on my recommendation, but recent updates to [uv](https://docs.astral.sh/uv/) have integrated the most important features. Rye's documentation notes: 

> If you're getting started with Rye, consider [uv](https://github.com/astral-sh/uv), the [successor project](https://lucumr.pocoo.org/2024/2/15/rye-grows-with-uv/) from the same maintainers.

> While Rye is actively maintained, uv offers a more stable and feature-complete experience, and is the recommended choice for new projects.

So for stability, more documentation, and support, we should probably migrate now while it's still early in our project.

Switching should be very easy, since Rye was using uv behind the scenes anyway and should already be installed for anyone using Rye. I'll get started on it now. 

Sorry for being just a little bit early! They released the version of uv with Rye features integrated like a month after I suggested it.

Fix patch:
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
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new file mode 100644
index 0000000..9d5dab7
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+sdist = { url = "https://files.pythonhosted.org/packages/56/fc/238c424fd7f4ebb25f8b1da9a934a3ad7c848286732ae04263661eb0fc03/widgetsnbextension-4.0.13.tar.gz", hash = "sha256:ffcb67bc9febd10234a362795f643927f4e0c05d9342c727b65d2384f8feacb6", size = 1164730 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/21/02/88b65cc394961a60c43c70517066b6b679738caf78506a5da7b88ffcb643/widgetsnbextension-4.0.13-py3-none-any.whl", hash = "sha256:74b2692e8500525cc38c2b877236ba51d34541e6385eeed5aec15a70f88a6c71", size = 2335872 },
+]


Test patch:
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