Temporary PR for testing devel

.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++]

docs/conf.py

@@ -78,7 +78,7 @@
 # }
 # html_logo = ''
 github_url = "https://github.com/PrincetonUniversity/SPECFEMPP"
-# html_baseurl = ''
+html_baseurl = 'https://specfem2d-kokkos.readthedocs.io/'
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,

docs/developer_documentation/SPECFEM_architecture/architecture.rst

@@ -1,7 +1,7 @@
 .. _architecture:
 
 SPECFEM++ Architecture
-====================
+======================
 
 SPECFEM++ is designed with portability and modularity as primary goals. The goal is develop a code that is easy to maintain and extend, while maintaining performance characteristics of original `SPECFEM2D solver <https://specfem2d.readthedocs.io>`_. This is achieved using C++ templatized classes.
 

docs/developer_documentation/git_workflow.rst

@@ -1,5 +1,5 @@
 Git development workflow
-=========================
+========================
 
 At SPECFEM++ we follow master-develop workflow. The master (main) branch is always a stable working code and is generally synced with the latest release of SPECFEM++. The develop branch is a stable code with potentially new features which haven't been released in the latest version of SPECFEM++ yet. If you are contributing to SPECFEM++ then issue your `pull request <https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests>`_ against the develop branch.
 
@@ -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.
 

docs/developer_documentation/style.rst

@@ -1,72 +1,62 @@
 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
-~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~
 
 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>`_.
 
 To enable the hooks (This only needs to be done when you clone the repo or there is an update to :code:`.pre-commit-config.yaml`)
 
 .. 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.
 
 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

docs/requirements.txt

@@ -1,3 +1,4 @@
+sphinx==8.0.0
 breathe
 furo
 sphinx-copybutton

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
 
 ```

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
 
 ```

examples/Tromp_2005/plot.py

@@ -7,12 +7,14 @@
 def load_data(directory):
     X = np.loadtxt(directory + "/ElasticIsotropic/X.txt")
     Z = np.loadtxt(directory + "/ElasticIsotropic/Z.txt")
-    rho = np.loadtxt(directory + "/ElasticIsotropic/rho.txt")
-    kappa = np.loadtxt(directory + "/ElasticIsotropic/kappa.txt")
-    mu = np.loadtxt(directory + "/ElasticIsotropic/mu.txt")
-    rhop = np.loadtxt(directory + "/ElasticIsotropic/rhop.txt")
-    alpha = np.loadtxt(directory + "/ElasticIsotropic/alpha.txt")
-    beta = np.loadtxt(directory + "/ElasticIsotropic/beta.txt")
+    data = np.loadtxt(directory + "/ElasticIsotropic/data.txt").reshape(6, X.shape[0])
+
+    rho = data[0, :]
+    mu = data[1, :]
+    kappa = data[2, :]
+    rhop = data[3, :]
+    alpha = data[4, :]
+    beta = data[5, :]
 
     return X, Z, rho, kappa, mu, rhop, alpha, beta
 
@@ -97,3 +99,7 @@ def plot_kernels(input_directory, output):
     plt.savefig(output, dpi=300)
 
     return
+
+
+if __name__ == "__main__":
+    plot_kernels("OUTPUT_FILES/Kernels", "Kernels_out.png")

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
 
 ```

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
 
 ```

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
 
 ```