Preparing for version alpha release

LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright 2025-2026 Jonathan Demaeyer
+Copyright 2025-2026 Jonathan Demaeyer and Oisín Hamilton
 
 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
 

README.md

@@ -23,15 +23,30 @@ LayerCake has been designed with geophysics in mind, although it may be useful f
 
 ## About
 
-(c) 2025-2026 Jonathan Demaeyer
+(c) 2025-2026 Jonathan Demaeyer and Oisín Hamilton
 
-See [LICENSE.txt](./LICENSE.txt) for license information.
+See [LICENSE.txt](https://github.com/Climdyn/LayerCake/blob/main/LICENSE.txt) for license information.
 
 ## Installation
 
 ### With pip
 
-Not yet available.
+The easiest way to install and run LayerCake is to use [pip](https://pypi.org/).
+Type in a terminal
+
+    pip install layercake-model
+
+and you are set!
+
+Additionally, you can clone the repository
+
+    git clone https://github.com/Climdyn/LayerCake.git
+
+and perform a test by running the script
+
+    python examples/atmospheric/barotropic_one_layer.py
+
+to see if everything runs smoothly (this should take less than 5 minutes).
 
 ### With Anaconda
 
@@ -64,12 +79,30 @@ To build the documentation, please run (with the conda environment activated):
 You may need to install [make](https://www.gnu.org/software/make/) if it is not already present on your system.
 Once built, the documentation is available [here](./documentation/build/html/index.html).
 
+The documentation is also available online at https://climdyn.github.io/LayerCake/. In particular, 
+please consider reading the [User guide](https://climdyn.github.io/LayerCake/files/user_guide.html#).
+
 ## Examples
 
 A few examples are available in the [examples](./examples) folder. More examples will be provided as the code is 
-developed.
+further developed.
+
+## Dependencies
+
+LayerCake needs mainly:
+
+* [Numpy](https://numpy.org/) for numeric support
+* [sparse](https://sparse.pydata.org/) for sparse multidimensional arrays support
+* [Numba](https://numba.pydata.org/) for code acceleration
+* [Sympy](https://www.sympy.org/) for symbolic manipulation of inner products
+
+Check the YAML file [environment.yml](https://raw.githubusercontent.com/Climdyn/LayerCake/main/environment.yml) for the dependencies.
 
 ## Contributing
 
 LayerCake is in beta development phase, bug reports and tests of the features are welcome.
 Please simply raise an issue on [Github](https://github.com/Climdyn/LayerCake/issues).
+
+If you want to contribute actively to the development, please contact the main authors.
+In addition, if you have made changes that you think will be useful to others, please feel free to suggest these as a pull request 
+on the [LayerCake Github repository](https://github.com/Climdyn/LayerCake/pulls).

documentation/source/files/general_information.rst

@@ -17,17 +17,32 @@ LayerCake has been designed with geophysics in mind, although it may be useful f
 About
 -----
 
-(c) 2025-2026 Jonathan Demaeyer
+© 2025-2026 Jonathan Demaeyer and Oisín Hamilton
 
-See `LICENSE.txt <../../../../LICENSE.txt>`_ for license information.
+See `LICENSE.txt <https://github.com/Climdyn/LayerCake/blob/main/LICENSE.txt>`_ for license information.
 
 Installation
 ------------
 
 With pip
 ~~~~~~~~
 
-Not yet available.
+The easiest way to install and run LayerCake is to use `pip <https://pypi.org/>`_.
+Type in a terminal ::
+
+    pip install layercake-model
+
+and you are set!
+
+Additionally, you can clone the repository ::
+
+    git clone https://github.com/Climdyn/LayerCake.git
+
+and perform a test by running the script ::
+
+    python examples/atmospheric/barotropic_one_layer.py
+
+to see if everything runs smoothly (this should take less than 5 minutes).
 
 With Anaconda
 ~~~~~~~~~~~~~
@@ -62,14 +77,39 @@ To build the documentation, please run (with the conda environment activated): :
 You may need to install `make <https://www.gnu.org/software/make/>`_ if it is not already present on your system.
 Once built, the documentation is available `here <../index.html>`_.
 
+The documentation is also available online at https://climdyn.github.io/LayerCake/. In particular,
+please consider reading the `User guide <https://climdyn.github.io/LayerCake/files/user_guide.html#>`_.
+
 Examples
 --------
 
 A few examples are available in the `examples <../../../../examples>`_ folder. More examples will be provided as the code is
-developed.
+further developed.
+
+Dependencies
+------------
+
+LayerCake needs mainly:
+
+
+* `Numpy`_ for numeric support
+* `sparse`_ for sparse multidimensional arrays support
+* `Numba`_ for code acceleration
+* `Sympy`_ for symbolic manipulation of inner products
+
+Check the YAML file `environment.yml <https://raw.githubusercontent.com/Climdyn/LayerCake/main/environment.yml>`_ for the dependencies.
 
 Contributing
 ------------
 
 LayerCake is in beta development phase, bug reports and tests of the features are welcome.
 Please simply raise an issue on `Github <https://github.com/Climdyn/LayerCake/issues>`_.
+
+If you want to contribute actively to the development, please contact the main authors.
+In addition, if you have made changes that you think will be useful to others, please feel free to suggest these as a pull request
+on the `LayerCake Github repository <https://github.com/Climdyn/LayerCake/pulls>`_.
+
+.. _Numba: https://numba.pydata.org/
+.. _Sympy: https://www.sympy.org/
+.. _sparse: https://sparse.pydata.org/
+.. _Numpy: https://numpy.org/

documentation/source/files/tricks.rst

@@ -152,7 +152,7 @@ variables:
 
   If this environment variable is not defined, then LayerCake default behavior is to use threads.
 * The :code:`LAYERCAKE_PARALLEL_INTEGRATION` environment variable controls the Sympy symbolic integration parallelization. If set to :code:`none`, the parallelization will be deactivated.
-  Otherwise, it will parallelized using processes.
+  Otherwise, it will be parallelized using processes.
   If this environment variable is not defined, then LayerCake default behavior is to parallelize using processes.
 
 For example,

layercake/__init__.py

@@ -12,3 +12,5 @@
 __all__ = ['Parameter', 'ParameterField', 'FunctionField', 'Field', 'Expression', 'SymbolicBasis', 'vorticity_advection', 'Jacobian',
            'OperatorTerm', 'ProductOfTerms', 'AdditionOfTerms', 'LinearTerm', 'ConstantTerm', 'Equation', 'Laplacian', 'D',
            'Layer', 'Cake']
+
+__version__ = '1.0.2a0'

pyproject.toml

@@ -0,0 +1,61 @@
+
+# pyproject.toml
+
+[build-system]
+requires = ["setuptools", "wheel"]
+
+[project]
+requires-python = ">=3.10"
+name = "layercake_model"
+version = "1.0.2-alpha"
+description = "A framework to design systems of partial differential equations (PDEs), and convert them to ordinary differential equations (ODEs) via Galerkin-type expansions. "
+readme = "README.md"
+authors = [
+    { name = "Jonathan Demaeyer", email = "jodemaey@meteo.be" },
+    { name = "Oisín Hamilton", email = "ush.hamilton@gmail.com" },
+]
+license = "BSD-3-Clause"
+license-files = [ "LICENSE.txt" ]
+classifiers = [
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "Operating System :: OS Independent",
+    "Development Status :: 4 - Beta",
+#    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Atmospheric Science",
+
+]
+keywords = ["pde", "symbolic-computation", "ode-model"]
+dependencies = [
+    "matplotlib",
+    "numpy",
+    "numba",
+    "scipy",
+    "sympy",
+    "sparse",
+    "pebble",
+]
+
+[project.urls]
+homepage = "https://github.com/Climdyn/LayerCake"
+documentation = "https://climdyn.github.io/LayerCake/"
+
+[tool.setuptools]
+packages = ["layercake",
+            "layercake.arithmetic",
+            "layercake.arithmetic.symbolic",
+            "layercake.arithmetic.terms",
+            "layercake.bakery",
+            "layercake.basis",
+            "layercake.formatters",
+            "layercake.inner_products",
+            "layercake.utils",
+            "layercake.variables",
+            ]