From f622eeee2ba4c06a91c6dbe2b3db0e07015746c8 Mon Sep 17 00:00:00 2001
From: ccui <ccui@princeton.edu>
Date: Wed, 5 Feb 2025 18:32:03 -0500
Subject: [PATCH 1/3] Migrate from poetry to uv

---
 .pre-commit-config.yaml                       |    2 +-
 docs/developer_documentation/git_workflow.rst |    4 +-
 docs/developer_documentation/style.rst        |   39 +-
 examples/README.md                            |   14 +-
 examples/Tromp_2005/README.md                 |   17 +-
 examples/fluid-solid-bathymetry/README.md     |   16 +-
 examples/fluid-solid-interface/README.md      |   16 +-
 .../README.md                                 |   17 +-
 examples/poetry.lock                          | 2241 -----------------
 examples/pyproject.toml                       |   20 -
 examples/solid-solid-interface/README.md      |   16 +-
 poetry.lock                                   | 1301 ----------
 pyproject.toml                                |   39 +-
 uv.lock                                       | 1830 ++++++++++++++
 14 files changed, 1909 insertions(+), 3663 deletions(-)
 delete mode 100644 examples/poetry.lock
 delete mode 100644 examples/pyproject.toml
 delete mode 100644 poetry.lock
 create mode 100644 uv.lock

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 125d7d8f5..fb51913bb 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -11,7 +11,7 @@ repos:
       - id: requirements-txt-fixer
       - id: trailing-whitespace
   - repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: "v15.0.6"
+    rev: "v19.1.7"
     hooks:
       - id: clang-format
         types_or: [c++]
diff --git a/docs/developer_documentation/git_workflow.rst b/docs/developer_documentation/git_workflow.rst
index 9dab12b98..46253122d 100644
--- a/docs/developer_documentation/git_workflow.rst
+++ b/docs/developer_documentation/git_workflow.rst
@@ -15,11 +15,11 @@ To make a change to SPECFEM++ (This development workflow is similar to the one s
 
 .. note::
 
-    It is also recommended that you run :code:`poetry install` every time you pull the develop branch. Please check :ref:`style section<style>` for more information on poetry.
+    It is also recommended that you run :code:`uv sync --extra dev` every time you pull the develop branch. Please check :ref:`style section<style>` for more information on uv.
 
 .. note::
 
-    Please also install pre-commit hooks after you've cloned repo. :code:`poetry run pre-commit install`
+    Please also install pre-commit hooks after you've cloned repo. :code:`uv run pre-commit install`
 
 - Next create a feature branch against develop branch called a feature branch. Please be explicit while naming the feature branch.
 
diff --git a/docs/developer_documentation/style.rst b/docs/developer_documentation/style.rst
index 66a2da4fd..ee2fb8813 100644
--- a/docs/developer_documentation/style.rst
+++ b/docs/developer_documentation/style.rst
@@ -4,53 +4,42 @@ Style
 Pre-commit
 ----------
 
-SPECFEM++ uses pre-commit to check style. Pre-commit can be installed inside python virtual environments. There are several methods for creating virtual environments, but I've found poetry tool is great at managing python environments. Especailly in collaborative environments poetry gives easy method for managing consistency of environments between all contributors via :code:`pyproject.toml` and :code:`poetry.lock` files.
+SPECFEM++ uses pre-commit to check style. Pre-commit can be installed inside python virtual environments. There are several methods for creating virtual environments, but I've found uv tool is great at managing python environments. Especailly in collaborative environments uv gives easy method for managing consistency of environments between all contributors via :code:`pyproject.toml` and :code:`uv.lock` files.
 
-Install poetry
+Install uv
 ~~~~~~~~~~~~~~~
 
-Download and install poetry using the `official instructions <https://python-poetry.org/docs/#installation>`_.
+Download and install uv using the `official instructions <https://docs.astral.sh/uv/getting-started/installation>`_.
 
 Install SPECFEM++ development environment
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 .. code-block:: bash
-
-    poetry install
+    uv sync --extra dev
 
 When you run this command one of two things happen,
 
-1. If a correct version of a package already exists within :code:`poetry.lock` file then poetry installs that version. Here the assumption is that a `poetry.lock` already exists, if not then one is created for you (within SPECFEM++ `poetry.lock` should already exist). `poetry.lock` ensures that all developers have consistent environments.
+1. If a correct version of a package already exists within :code:`uv.lock` file then uv installs that version. Here the assumption is that a `uv.lock` already exists, if not then one is created for you (within SPECFEM++ `uv.lock` should already exist). `uv.lock` ensures that all developers have consistent environments.
 
-2. If a correct version of a package doesn't exist within :code:`poetry.lock` then poetry will install a correct version and update `poetry.lock` file.
+2. If a correct version of a package doesn't exist within :code:`uv.lock` then uv will install a correct version and update `uv.lock` file.
 
 .. note::
 
-    Make sure you commit :code:`poetry.lock` and :code:`pyproject.toml` files upstream to the remote if you add any packages.
+    Make sure you commit :code:`uv.lock` and :code:`pyproject.toml` files upstream to the remote if you add any packages.
 
 .. note::
 
-    It is also recommended that you run :code:`poetry install` every time you pull the develop branch
+    It is also recommended that you run :code:`uv sync --extra dev` every time you pull the develop branch
 
-Using your python/poetry environment
+Using your python/uv environment
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-If you're in the SPECFEM++ root directory you should have access to the poetry environment. To run a command within the environment either
-
-1. Explicitly activate the environment using :code:`poetry shell` as shown below
-
-.. code-block:: bash
-
-    poetry shell
-    python <script_name>.py
-
-Or
-
-2. Directly run the command within environment using :code:`poetry run`
+If you're in the SPECFEM++ root directory with an IDE with Python support, you should have access to the uv environment directly.
+To explicitly activate the environment, you can run the following command
 
 .. code-block:: bash
 
-    poetry run python <script_name>.py
+    source .venv/bin/activate
 
 Pre-commit hooks
 ~~~~~~~~~~~~~~~~~
@@ -61,7 +50,7 @@ To enable the hooks (This only needs to be done when you clone the repo or there
 
 .. code-block:: bash
 
-    poetry run pre-commit install
+    uv run pre-commit install
 
 After this, pre-commit should run every time you commit a change. Ensuring that coding style is consistent across all developers.
 
@@ -69,4 +58,4 @@ To manually run pre-commit on all files
 
 .. code-block:: bash
 
-    poetry run pre-commit run --all-files
+    uv run pre-commit run --all-files
diff --git a/examples/README.md b/examples/README.md
index dd5bce60f..a10d5eb54 100644
--- a/examples/README.md
+++ b/examples/README.md
@@ -8,14 +8,14 @@ The examples use [snakemake](https://snakemake.readthedocs.io/en/stable/) to run
 
 ## Running the examples
 
-To run the examples, you first need to install poetry following these [instructions](https://python-poetry.org/docs/#installation). Once you've done so, you can install the dependencies for the examples by running the following command in the current directory:
+To run the examples, you first need to install uv following these [instructions](https://docs.astral.sh/uv/getting-started/installation). Once you've done so, you can install the dependencies for the examples by running the following command in the current directory:
 
 ```bash
-# verify poetry is installed
-poetry --version
+# verify uv is installed
+uv --version
 
 # install dependencies
-poetry install
+uv sync --extra examples
 
 ```
 
@@ -26,10 +26,10 @@ After installing the dependencies, you can run the examples by running the follo
 cd <example directory>
 
 # run the example
-poetry run snakemake -j 1
+uv run snakemake -j 1
 
 # or to run the example on a slurm cluster
-poetry run snakemake --executor slurm -j 1
+uv run snakemake --executor slurm -j 1
 
 ```
 
@@ -40,6 +40,6 @@ To clean up the example directory, you can run the following command in the dire
 ```bash
 
 # clean up the example
-poetry run snakemake clean
+uv run snakemake clean -j 1
 
 ```
diff --git a/examples/Tromp_2005/README.md b/examples/Tromp_2005/README.md
index 99a6552b0..6abc431ae 100644
--- a/examples/Tromp_2005/README.md
+++ b/examples/Tromp_2005/README.md
@@ -4,14 +4,17 @@ This example reproduces the results from Fig 9 of [Tromp et al. 2005](https://do
 
 ## Running the examples
 
-To run the examples, you first need to install poetry following these [instructions](https://python-poetry.org/docs/#installation). Once you've done so, you can install the dependencies for the examples by running the following command in the current directory:
+To run the examples, you first need to install uv following these
+[instructions](https://docs.astral.sh/uv/getting-started/installation). Once you've done
+so, you can install the dependencies for the examples by running the following
+command in the current directory:
 
 ```bash
-# verify poetry is installed
-poetry --version
+# verify uv is installed
+uv --version
 
 # install dependencies
-poetry install
+uv sync --extra examples
 
 ```
 
@@ -22,10 +25,10 @@ After installing the dependencies, you can run the examples by running the follo
 cd <example directory>
 
 # run the example
-poetry run snakemake -j 1
+uv run snakemake -j 1
 
 # or to run the example on a slurm cluster
-poetry run snakemake --executor slurm -j 1
+uv run snakemake --executor slurm -j 1
 
 ```
 
@@ -36,6 +39,6 @@ To clean up the example directory, you can run the following command in the dire
 ```bash
 
 # clean up the example
-poetry run snakemake clean
+uv run snakemake clean -j 1
 
 ```
diff --git a/examples/fluid-solid-bathymetry/README.md b/examples/fluid-solid-bathymetry/README.md
index d69f88570..e6dfa6f51 100644
--- a/examples/fluid-solid-bathymetry/README.md
+++ b/examples/fluid-solid-bathymetry/README.md
@@ -7,17 +7,17 @@ publication [Pipatprathanporn et al.
 
 ## Running the examples
 
-To run the examples, you first need to install poetry following these
-[instructions](https://python-poetry.org/docs/#installation). Once you've done
+To run the examples, you first need to install uv following these
+[instructions](https://docs.astral.sh/uv/getting-started/installation). Once you've done
 so, you can install the dependencies for the examples by running the following
 command in the current directory:
 
 ```bash
-# verify poetry is installed
-poetry --version
+# verify uv is installed
+uv --version
 
 # install dependencies
-poetry install
+uv sync --extra examples
 
 ```
 
@@ -27,10 +27,10 @@ following command within the example directory you want to run:
 ```bash
 
 # run the example
-poetry run snakemake -j 1
+uv run snakemake -j 1
 
 # or to run the example on a slurm cluster
-poetry run snakemake --executor slurm -j 1
+uv run snakemake --executor slurm -j 1
 
 ```
 
@@ -68,6 +68,6 @@ directory of the example you want to clean up:
 ```bash
 
 # clean up the example
-poetry run snakemake clean
+uv run snakemake clean -j 1
 
 ```
diff --git a/examples/fluid-solid-interface/README.md b/examples/fluid-solid-interface/README.md
index f2dd2dfd7..a6ffe7238 100644
--- a/examples/fluid-solid-interface/README.md
+++ b/examples/fluid-solid-interface/README.md
@@ -7,17 +7,17 @@ guide on this example, please refer to the
 
 ## Running the examples
 
-To run the examples, you first need to install poetry following these
-[instructions](https://python-poetry.org/docs/#installation). Once you've done
+To run the examples, you first need to install uv following these
+[instructions](https://docs.astral.sh/uv/getting-started/installation). Once you've done
 so, you can install the dependencies for the examples by running the following
 command in the current directory:
 
 ```bash
-# verify poetry is installed
-poetry --version
+# verify uv is installed
+uv --version
 
 # install dependencies
-poetry install
+uv sync --extra examples
 
 ```
 
@@ -27,10 +27,10 @@ following command within the example directory you want to run:
 ```bash
 
 # run the example
-poetry run snakemake -j 1
+uv run snakemake -j 1
 
 # or to run the example on a slurm cluster
-poetry run snakemake --executor slurm -j 1
+uv run snakemake --executor slurm -j 1
 
 ```
 
@@ -42,6 +42,6 @@ directory of the example you want to clean up:
 ```bash
 
 # clean up the example
-poetry run snakemake clean
+uv run snakemake clean -j 1
 
 ```
diff --git a/examples/homogeneous-medium-flat-topography/README.md b/examples/homogeneous-medium-flat-topography/README.md
index a7245b098..94acf064b 100644
--- a/examples/homogeneous-medium-flat-topography/README.md
+++ b/examples/homogeneous-medium-flat-topography/README.md
@@ -4,14 +4,17 @@ In this example we simulate wave propagation through a 2-dimensional homogeneous
 
 ## Running the examples
 
-To run the examples, you first need to install poetry following these [instructions](https://python-poetry.org/docs/#installation). Once you've done so, you can install the dependencies for the examples by running the following command in the current directory:
+To run the examples, you first need to install uv following these
+[instructions](https://docs.astral.sh/uv/getting-started/installation). Once you've done
+so, you can install the dependencies for the examples by running the following
+command in the current directory:
 
 ```bash
-# verify poetry is installed
-poetry --version
+# verify uv is installed
+uv --version
 
 # install dependencies
-poetry install
+uv sync --extra examples
 
 ```
 
@@ -20,10 +23,10 @@ After installing the dependencies, you can run the examples by running the follo
 ```bash
 
 # run the example
-poetry run snakemake -j 1
+uv run snakemake -j 1
 
 # or to run the example on a slurm cluster
-poetry run snakemake --executor slurm -j 1
+uv run snakemake --executor slurm -j 1
 
 ```
 
@@ -34,6 +37,6 @@ To clean up the example directory, you can run the following command in the dire
 ```bash
 
 # clean up the example
-poetry run snakemake clean
+uv run snakemake clean -j 1
 
 ```
diff --git a/examples/poetry.lock b/examples/poetry.lock
deleted file mode 100644
index 5b084a1fb..000000000
--- a/examples/poetry.lock
+++ /dev/null
@@ -1,2241 +0,0 @@
-# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand.
-
-[[package]]
-name = "appdirs"
-version = "1.4.4"
-description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
-optional = false
-python-versions = "*"
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-    {file = "appdirs-1.4.4.tar.gz", hash = "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41"},
-]
-
-[[package]]
-name = "argparse-dataclass"
-version = "2.0.0"
-description = "Declarative CLIs with argparse and dataclasses"
-optional = false
-python-versions = ">=3.8"
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-    {file = "argparse_dataclass-2.0.0.tar.gz", hash = "sha256:09ab641c914a2f12882337b9c3e5086196dbf2ee6bf0ef67895c74002cc9297f"},
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-
-[[package]]
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-[[package]]
-name = "yte"
-version = "1.5.5"
-description = "A YAML template engine with Python expressions"
-optional = false
-python-versions = ">=3.7"
-files = [
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-
-[package.dependencies]
-dpath = ">=2.1,<3.0"
-plac = ">=1.3.4,<2.0.0"
-pyyaml = ">=6.0,<7.0"
-
-[metadata]
-lock-version = "2.0"
-python-versions = "^3.12"
-content-hash = "74971bb35df48c7ad650209658991f98e18bf9211a17180645f80cf14ff10338"
diff --git a/examples/pyproject.toml b/examples/pyproject.toml
deleted file mode 100644
index 24f8bfa5b..000000000
--- a/examples/pyproject.toml
+++ /dev/null
@@ -1,20 +0,0 @@
-[tool.poetry]
-name = "SPECFEMPP_EXAMPLES"
-version = "0.1.0"
-description = ""
-authors = ["Rohit Kakodkar <kakodkar.rohit@gmail.com>"]
-
-[tool.poetry.dependencies]
-python = "^3.12"
-snakemake = "^8.14.0"
-obspy = "^1.4.0"
-snakemake-executor-plugin-slurm = "^0.10.0"
-imageio = "^2.36.1"
-jinja2 = ">=3.1.4"
-PyYAML = ">=6.0.2"
-
-[tool.poetry.dev-dependencies]
-
-[build-system]
-requires = ["poetry-core>=1.0.0"]
-build-backend = "poetry.core.masonry.api"
diff --git a/examples/solid-solid-interface/README.md b/examples/solid-solid-interface/README.md
index a46b9c7a8..1b5e4c27d 100644
--- a/examples/solid-solid-interface/README.md
+++ b/examples/solid-solid-interface/README.md
@@ -8,17 +8,17 @@ For a step-by-step guide on this example, please refer to the
 
 ## Running the examples
 
-To run the examples, you first need to install poetry following these
-[instructions](https://python-poetry.org/docs/#installation). Once you've done
+To run the examples, you first need to install uv following these
+[instructions](https://docs.astral.sh/uv/getting-started/installation). Once you've done
 so, you can install the dependencies for the examples by running the following
 command in the current directory:
 
 ```bash
-# verify poetry is installed
-poetry --version
+# verify uv is installed
+uv --version
 
 # install dependencies
-poetry install
+uv sync --extra examples
 
 ```
 
@@ -28,10 +28,10 @@ following command within the example directory you want to run:
 ```bash
 
 # run the example
-poetry run snakemake -j 1
+uv run snakemake -j 1
 
 # or to run the example on a slurm cluster
-poetry run snakemake --executor slurm -j 1
+uv run snakemake --executor slurm -j 1
 
 ```
 
@@ -43,6 +43,6 @@ directory of the example you want to clean up:
 ```bash
 
 # clean up the example
-poetry run snakemake clean
+uv run snakemake clean -j 1
 
 ```
diff --git a/poetry.lock b/poetry.lock
deleted file mode 100644
index 0b84c0960..000000000
--- a/poetry.lock
+++ /dev/null
@@ -1,1301 +0,0 @@
-# This file is automatically @generated by Poetry 2.0.0 and should not be changed by hand.
-
-[[package]]
-name = "alabaster"
-version = "0.7.16"
-description = "A light, configurable Sphinx theme"
-optional = false
-python-versions = ">=3.9"
-groups = ["main"]
-files = [
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-    {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"},
-]
-
-[[package]]
-name = "annotated-types"
-version = "0.7.0"
-description = "Reusable constraint types to use with typing.Annotated"
-optional = false
-python-versions = ">=3.8"
-groups = ["main"]
-files = [
-    {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"},
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-docs = ["breathe", "doc8", "furo", "restructuredtext-lint", "rstcheck", "sphinx-copybutton", "sphinx-rtd-theme", "sphinx-sitemap"]
-
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-python-versions = ">=3.12,<4.0"
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diff --git a/pyproject.toml b/pyproject.toml
index 79ac4e363..862ebeb4e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,11 +17,8 @@ requires-python = ">=3.12"
 [project.optional-dependencies]
 dev = [
   "pre-commit~=2.19.0",
-  "clang-format~=15.0.6",
-  "ruff>=0.6.7"
-]
-
-docs = [
+  "clang-format~=19.1.7",
+  "ruff>=0.9.1",
   "sphinx-rtd-theme~=1.3.0",
   "doc8>=0.3.6",
   "rstcheck>=6.2.4",
@@ -32,6 +29,15 @@ docs = [
   "sphinx-sitemap~=2.2.0"
 ]
 
+examples = [
+  "snakemake~=8.14.0",
+  "obspy~=1.4.0",
+  "snakemake-executor-plugin-slurm~=0.10.0",
+  "imageio~=2.36.1",
+  "jinja2>=3.1.4",
+  "PyYAML>=6.0.2"
+]
+
 [tool.scikit-build]
 cmake.define.CMAKE_BUILD_TYPE = "Release"
 cmake.define.BUILD_TESTS = "ON"
@@ -39,26 +45,3 @@ cmake.define.SPECFEMPP_USE_SKBUILD = "ON"
 cmake.define.SPECFEMPP_BINDING_PYTHON = "ON"
 build-dir = "./build"
 build.tool-args = ["-j4"]
-
-[tool.poetry]
-package-mode = false
-
-[tool.poetry.dependencies]
-python = ">=3.12,<4.0"
-pre-commit = "^2.19.0"
-clang-format = "^15.0.6"
-sphinx-rtd-theme = "^1.0.0"
-doc8 = ">=0.3.6"
-rstcheck = ">=6.2.4"
-restructuredtext-lint = ">=1.4.0"
-sphinx-copybutton = "^0.4.0"
-furo = ">=2024.8.6"
-breathe = "^4.34.0"
-sphinx-sitemap = "^2.2.0"
-ruff = ">=0.6.7"
-
-[tool.poetry.dev-dependencies]
-
-[tool.snakefmt]
-line_length = 90
-include = '\.smk$|^Snakefile|\.py|^Snakefile.in$'
diff --git a/uv.lock b/uv.lock
new file mode 100644
index 000000000..604b51a2b
--- /dev/null
+++ b/uv.lock
@@ -0,0 +1,1830 @@
+version = 1
+requires-python = ">=3.12"
+
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+version = "0.7.16"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/c9/3e/13dd8e5ed9094e734ac430b5d0eb4f2bb001708a8b7856cbf8e084e001ba/alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65", size = 23776 }
+wheels = [
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+]
+
+[[package]]
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+version = "0.7.0"
+source = { registry = "https://pypi.org/simple" }
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From d10e107142648f52d6f5e108521c56af613a3148 Mon Sep 17 00:00:00 2001
From: ccui <ccui@princeton.edu>
Date: Thu, 6 Feb 2025 09:40:12 -0500
Subject: [PATCH 2/3] Avoid automatic building

---
 pyproject.toml | 5 ++++-
 uv.lock        | 4 ++--
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 862ebeb4e..b471eb727 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "scikit_build_core.build"
 
 [project]
 name = "specfempp_core"
-version = "0.1.0"
+version = "0.3.0"
 description = "Kokkos implementation of SpecFEM2D code"
 readme = "README.md"
 authors = [
@@ -14,6 +14,9 @@ authors = [
 ]
 requires-python = ">=3.12"
 
+[tool.uv]
+package = false
+
 [project.optional-dependencies]
 dev = [
   "pre-commit~=2.19.0",
diff --git a/uv.lock b/uv.lock
index 604b51a2b..453f4c596 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1459,8 +1459,8 @@ wheels = [
 
 [[package]]
 name = "specfempp-core"
-version = "0.1.0"
-source = { editable = "." }
+version = "0.3.0"
+source = { virtual = "." }
 
 [package.optional-dependencies]
 dev = [

From 8bc81f5f90049852549679c6e546e576413d7f44 Mon Sep 17 00:00:00 2001
From: ccui <ccui@princeton.edu>
Date: Fri, 7 Feb 2025 15:47:25 -0500
Subject: [PATCH 3/3] Update docs for uv.

---
 docs/developer_documentation/style.rst | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/docs/developer_documentation/style.rst b/docs/developer_documentation/style.rst
index ee2fb8813..5c7362fd8 100644
--- a/docs/developer_documentation/style.rst
+++ b/docs/developer_documentation/style.rst
@@ -7,14 +7,15 @@ Pre-commit
 SPECFEM++ uses pre-commit to check style. Pre-commit can be installed inside python virtual environments. There are several methods for creating virtual environments, but I've found uv tool is great at managing python environments. Especailly in collaborative environments uv gives easy method for managing consistency of environments between all contributors via :code:`pyproject.toml` and :code:`uv.lock` files.
 
 Install uv
-~~~~~~~~~~~~~~~
+~~~~~~~~~~
 
 Download and install uv using the `official instructions <https://docs.astral.sh/uv/getting-started/installation>`_.
 
 Install SPECFEM++ development environment
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 .. code-block:: bash
+
     uv sync --extra dev
 
 When you run this command one of two things happen,
@@ -32,7 +33,7 @@ When you run this command one of two things happen,
     It is also recommended that you run :code:`uv sync --extra dev` every time you pull the develop branch
 
 Using your python/uv environment
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 If you're in the SPECFEM++ root directory with an IDE with Python support, you should have access to the uv environment directly.
 To explicitly activate the environment, you can run the following command
@@ -42,7 +43,7 @@ To explicitly activate the environment, you can run the following command
     source .venv/bin/activate
 
 Pre-commit hooks
-~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~
 
 Next, we install pre-commit hooks to check style. Pre-commit hooks are defined in :code:`.pre-commit-config.yaml` within SPECFEM++ root directory. More documentation on pre-commit hooks can be found `here <https://pre-commit.com/hooks.html>`_.