Cpt conditioning continued

.flake8

@@ -0,0 +1,4 @@
+[flake8]
+ignore = F403, F405, W503, W504
+max-line-length = 120
+per-file-ignores = __init__.py:F401

.github/workflows/tests.yml

@@ -2,10 +2,11 @@ name: Tests
 
 # Controls when the workflow will run
 on:
-  push:
-    branches: [ "**" ]
   pull_request:
-    branches: [ "main" ]
+    branches: [ "**" ]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
 
 jobs:
   test:

.gitignore

@@ -6,4 +6,5 @@ pytest_cache/*
 build/*
 random_fields.egg-info/*
 .coverage
-.tox/*
+.tox/*
+docs/build/*

.pre-commit-config.yaml

@@ -0,0 +1,21 @@
+repos:
+  - repo: local
+    hooks:
+      - id: yapf
+        name: yapf
+        language: python
+        entry: yapf
+        args: [-i]
+        types: [python]
+      - id: mypy
+        name: mypy
+        language: python
+        entry: mypy
+        files: "^random_fields/"
+        args: [ --config-file, "pyproject.toml" ]
+        types: [python]
+      - id: flake8
+        name: flake8
+        language: python
+        entry: flake8
+        files: "^random_fields/"

.readthedocs.yaml

@@ -0,0 +1,28 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version, and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+  jobs:
+    pre_build:
+    - sphinx-apidoc -o docs ./random_fields
+    - pip install .
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+# Optionally, but recommended,
+# declare the Python requirements required to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+   install:
+   - requirements: docs/requirements.txt
+
+

.style.yapf

@@ -0,0 +1,12 @@
+[style]
+based_on_style = pep8
+SPLIT_ALL_TOP_LEVEL_COMMA_SEPARATED_VALUES = False
+dedent_closing_brackets = False
+EACH_DICT_ENTRY_ON_SEPARATE_LINE = True
+FORCE_MULTILINE_DICT = False
+coalesce_brackets = True
+column_limit = 120
+split_arguments_when_comma_terminated = True
+SPLIT_BEFORE_FIRST_ARGUMENT = False
+#SPLIT_PENALTY_FOR_ADDED_LINE_SPLIT = 1
+ALLOW_SPLIT_BEFORE_DICT_VALUE = False

README.md

@@ -75,7 +75,7 @@ plot2D([np.array([x.ravel(), y.ravel()]).T], [rf.random_field], title="Random Fi
 
 The result is the following random field:
 
-![Random field 2D](./docs/static/random_field.png)
+![Random field 2D](./docs/_static/random_field.png)
 
 ## Example in 3D
 
@@ -127,4 +127,4 @@ plot3D([np.array([x.ravel(), y.ravel(), z.ravel()]).T], [rf.random_field], title
 ```
 The result is the following random field:
 
-![Random field 3D](./docs/static/random_field_3D.png)
+![Random field 3D](./docs/_static/random_field_3D.png)

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/authors.rst

@@ -0,0 +1,14 @@
+.. _authors:
+
+Random Fields team
+==================
+
+Maintainers
+-----------
+- Bruno Zuada Coelho <bruno.zuadacoelho@deltares.nl> `@brunozc <https://github.com/brunozc>`_
+- Aron Noordam <aron.noordam@deltares.nl> `@aronnoordam <https://github.com/aronnoordam>`_
+
+Developers
+----------
+- Bram van den Eijnden <bram.vandneeijnden@deltares.nl> `@bramvandeneijnden <https://github.com/bramvandeneijnden>`_
+- Davide Moretti <davide.moretti@tno.nl> `@morettid <https://github.com/morettid>`_

docs/conf.py

@@ -0,0 +1,60 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+import random_fields
+
+project = 'RandomFields'
+copyright = '2024, STEM team'
+author = 'STEM team'
+version = random_fields.__version__
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ['sphinx.ext.autodoc', 'sphinx_rtd_theme', 'sphinx.ext.intersphinx']
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+# to add __init__ documentation to the build
+autoclass_content = 'both'
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'sphinx_rtd_theme'
+html_static_path = ['_static']
+
+# # Configure the RTD theme options
+html_theme_options = {
+    'logo_only': False,
+    'display_version': True,
+    'prev_next_buttons_location': 'bottom',
+    'style_external_links': True,  # Toc options
+    'collapse_navigation': False,
+    'sticky_navigation': True,
+    'navigation_depth': 2,
+    'includehidden': True,
+    'titles_only': True,
+}
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+html_show_sphinx = False
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+html_show_copyright = True
+# If true shows the source link to the rst code
+html_show_sourcelink = False
+
+# Link to the github
+html_context = {
+    "display_github": True,
+    "github_user": "StemVibrations",
+    "github_repo": "RandomFields",
+    "github_version": "main",
+    "conf_py_path": "/docs/",
+}

docs/contributions.rst

@@ -0,0 +1,111 @@
+Code contribution
+=================
+
+Steps for submitting your code
+------------------------------
+
+When contributing code follow this checklist:
+
+    #. Fork the repository on GitHub.
+    #. Create an issue with the desired feature or bug fix.
+    #. Make your modifications or additions in a feature branch.
+    #. Make changes and commit your changes using a descriptive commit message.
+    #. Provide tests for your changes, and ensure they all pass.
+    #. Provide documentation for your changes, in accordance with the style of the rest of the project (see :ref:`style_guide`).
+    #. Create a pull request to RandomFields main branch. The STEM team will review and discuss your Pull Request with you.
+
+For any questions, please get in contact with one of the members of :doc:`authors`.
+
+
+.. _style_guide:
+
+Code style guide
+----------------
+The additional features should follow the style of the RandomFields project.
+
+We follow the PEP 8 style guide for Python code, with our custom modifications as defined in the
+`Yapf file <../../.style.yapf>`_ and the `flake8 file <../../.flake8>`_. These files can be ran manually by using the
+following command from the root directory of the project:
+
+.. code-block::
+
+    pre-commit run --all-files
+
+
+The class or function name should be clear and descriptive of the functionality it provides.
+
+There should be a docstring at the beginning of the class or function describing its purpose and usage.
+The docstring should be in the form of a triple-quoted string.
+
+The class or function must have a type annotation.
+The class should specify the attributes and inheritance.
+The function should specify the arguments, exceptions and returns (in this order).
+The return type annotation should be in the form of a comment after the closing parenthesis of the arguments.
+
+Please, avoid inheritance, and favour composition when writing your code.
+
+An example of a class:
+
+.. code-block::
+
+    class ClassName(object):
+        """
+        Work in progress: docstring style to be specified
+
+        Inheritance:
+            -:class:`object`
+
+        Attributes:
+            - <attribute_name_1> (<attribute type>): <attribute description>,shape (n,m)
+            - <attribute_name_2> (<attribute type>): <attribute description>,shape (m,)
+
+
+        """
+        def __init__(self,<args>,...):
+            """
+            Constructor of the RandomFields class
+
+            Args:
+                - <arg>: (<type>) <description>, shape (n,m,), default
+            """
+            self.attribute_name_1: <attribute_type> = <value>
+            self.attribute_name_2: <attribute_type> = <value>
+
+
+An example of a function:
+
+.. code-block::
+
+    def generate(self, nodes: npt.NDArray[np.float64]) -> None:
+        """
+        Generate random field
+
+        Args:
+            - nodes (ndarray): The nodes of the random field. shape (:,`self.n_dim`)
+
+        Raises:
+            - ValueError: if dimensions of `nodes` do not match dimensions of the model
+
+        Returns:
+
+        """
+
+        # check dimensions of nodes agrees with dimensions of model
+        if nodes.shape[1] != self.n_dim:
+            raise ValueError(f'Dimensions of nodes: {nodes.shape[1]} do not match dimensions of model: {self.n_dim}')
+
+        # scale of fluctuation
+        scale_fluctuation = np.ones(self.n_dim) * self.vertical_scale_fluctuation
+
+        # apply the anisotropy to the other dimensions
+        mask = np.arange(len(scale_fluctuation)) != self.v_dim
+        scale_fluctuation[mask] = scale_fluctuation[mask] * self.anisotropy
+
+        model = self.random_field_model(dim = self.n_dim,
+                                        var = self.variance,
+                                        len_scale = scale_fluctuation,
+                                        angles = self.angle)
+        self.random_field = gs.SRF(model,
+                                   mean = self.mean,
+                                   seed = self.seed)
+        self.random_field(nodes.T)

docs/index.rst

@@ -0,0 +1,60 @@
+RandomFields
+====
+Python package to generate random fields in 2D or 3D on unstructured grids.
+
+
+User guide
+==========
+
+Background information
+......................
+The random fields are generated using `gstools <https://geostat-framework.readthedocs.io/en/latest/>`_.
+
+Currently, the following covariance models are available:
+
+* Gaussian
+* Exponential
+* Matern
+* Linear (not for conditioned random fields)
+
+Additional functionalities are used to generate conditioned random fields.
+
+
+Tutorials
+.........
+
+* :ref:`tutorial1`
+    1D unconditioned and conditioned random field generation.
+
+* :ref:`tutorial2`
+    2D unconditioned and conditioned random field simulation.
+
+* :ref:`tutorial3`
+    3D unconditioned and conditioned random field simulation.
+
+* :ref:`tutorial4`
+    Non-normal Gaussian fields and conditioning based on CPT data.
+
+
+How to contribute
+=================
+If you want to contribute to RandomFields please follow the steps defined in :doc:`contributions`.
+
+
+Random Fields team
+==================
+The Random Field package is part of the STEM is a research programme that results from a
+collaboration between the following partners:
+
+* `ProRail <https://www.prorail.nl>`_
+* `Deltares <https://www.deltares.nl>`_
+* `TNO <https://www.tno.nl>`_
+* `TU Delft <https://www.tudelft.nl>`_
+
+The :doc:`authors`.
+
+
+Package documentation
+=====================
+
+The :doc:`random_fields` documentation.

docs/installation.rst

@@ -0,0 +1,10 @@
+RandomFields installation
+=================
+
+.. _python_random_fields:
+
+RandomFields Python package
+-------------------
+
+
+To be copied from STEM