Refactor to make it an installable package with a CLI

.gitignore

@@ -0,0 +1,207 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py.cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+#poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+#pdm.lock
+#pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+#pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.envrc
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Abstra
+# Abstra is an AI-powered process automation framework.
+# Ignore directories containing user credentials, local state, and settings.
+# Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#  and can be added to the global gitignore or merged into this file. However, if you prefer,
+#  you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Cursor
+#  Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/

.pre-commit-config.yaml

@@ -0,0 +1,42 @@
+repos:
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v4.1.0
+      hooks:
+          - id: double-quote-string-fixer
+          - id: end-of-file-fixer
+            exclude: &exclude >-
+                (?x)^(
+                    tests/.*fixtures|
+                    .*\.json|
+                    .*\.txt
+                )$
+          - id: mixed-line-ending
+          - id: trailing-whitespace
+            exclude: *exclude
+
+    - repo: https://github.com/ikamensh/flynt/
+      rev: "0.76"
+      hooks:
+          - id: flynt
+
+    - repo: https://github.com/pycqa/isort
+      rev: "5.12.0"
+      hooks:
+          - id: isort
+            exclude: *exclude
+
+    # - repo: local
+    #   hooks:
+    #       - id: pylint
+    #         name: pylint
+    #         entry: pylint
+    #         language: system
+    #         types: [python]
+    #         exclude: >
+    #             (?x)^(
+    #                 manage\.py|
+    #                 mysite/.*|
+    #                 .*/migrations/.*|
+    #                 docs/.*|
+    #                 tests/.*(?<!\.py)$
+    #             )$

README.md

@@ -2,10 +2,12 @@
 
 This project contains code for simulating infiltration processes in porous materials using the FEniCSx finite element framework.
 
-## Files
+## Install
 
-- **`data.py`** - Configuration file containing input parameters for the simulation
-- **`infiltration.py`** - Main simulation script implementing the infiltration model
+```bash
+cd <PATH to folder with pyproject.toml>
+pip install .
+```
 
 ## Description
 
@@ -23,34 +25,69 @@ The simulation models capillary infiltration in porous media using:
 - **Solver**: Newton-Raphson with adaptive timestepping
 - **Output**: VTX files for visualization and numpy arrays for data analysis
 
-## Requirements
+## External Requirements
+
+Packages not installable via `pip`:
 
-This project requires FEniCSx and related dependencies with:
-- `fenics-dolfinx` - Main FEniCS library
-- `petsc4py` - Parallel linear algebra
-- `mpi4py` - Message passing interface
-- `matplotlib` - Plotting and visualization
-- `numpy` - Numerical computing
-- `tqdm` - Progress bars
+- `fenics-dolfinx==0.9.0` - Main FEniCS library + Python bindings
 
 ## Usage
 
-Run the simulation by providing the parameter file:
+### Progamatically
+
+Example.
+
+```python
+from aitw_darcy.data import Params
+from aitw_darcy.infiltration import run_simulation
+
+params = Params()
+params.XXX = YYY  # Set parameters as needed
+
+run_simulation(params)
+```
+
+### CLI
+
+The installation will make available a `aitw-darcy` command line interface.
+
+- Run `aitw-darcy --help` to see the available commands.
+- Run `aitw-darcy infiltration --help` to see all available options for running the simulation.
+- Run `aitw-darcy infiltration INPUT_JSON_FILE` to run the simulation using the parameters in `JSON_FILE`.
+
+Example with the provided parameter file:
 
 ```bash
-python infiltration.py data.py
+aitw-darcy infiltration example/input.json
 ```
 
+#### Tab autocompletion
+
+Enabling tab autocompletion https://click.palletsprojects.com/en/stable/shell-completion/
+
+E.G for `bash` run the command
+
+```bash
+eval "$(_AITW_DARCY_MS_COMPLETE=bash_source aitw-darcy)"
+```
+
+You can also add it to either `~/.bashrc` or, if you are using a virtual environment, to `bin/activate` of the virtual environment to avoid running the command for every new shell.
+
 ## Output
 
-The simulation generates:
+The simulation generates the following output files in the specified output directory:
+
 - `{label}_solution.npy` - Complete solution array for analysis
 - `{label}_output.bp` - VTX mesh files for ParaView visualization
 - `{label}.log` - Simulation log file
+- `reprod.json` - Copy of the input parameters for reproducibility
+
+where `{label}` is defined in the input parameters.
 
 ## Parameters
 
-Key simulation parameters (configurable in `data.py`):
+Key simulation parameters:
+
 - Mesh dimensions and resolution
 - Material properties (porosity, permeability, surface tension)
 - Fluid properties (viscosity, contact angle)

aitw_darcy/__init__.py

@@ -0,0 +1,2 @@
+"""AITW Darcy Module TODO: improve description"""
+__version__ = '0.1.0'

aitw_darcy/cli/__init__.py

@@ -0,0 +1,28 @@
+import click as original_click
+import rich_click as click
+from rich.traceback import install
+
+install(
+    suppress=[original_click, click],
+)
+
+@click.group('aitw-darcy')
+def cmd_root():
+    """ Command line interface for AITW Darcy simulations """
+    pass
+
+@cmd_root.command()
+@click.argument('json_file', required=True, type=click.Path(exists=True))
+@click.option('--output_dir', type=click.Path(), help='Output directory')
+def infiltration(
+        json_file: str,
+        output_dir: str = '.',
+    ):
+    """ Run the infiltration simulation command line interface """
+    from aitw_darcy.data import Params
+    from aitw_darcy.infiltration import run_simulation
+
+    params = Params.from_json(json_file)
+    if output_dir is not None:
+        params.output_dir = output_dir
+    run_simulation(params)