lsapy 0.3.0__tar.gz → 0.4.0__tar.gz

{lsapy-0.3.0 → lsapy-0.4.0}/CHANGELOG.rst

@@ -2,13 +2,63 @@
 Changelog
 =========
 
-v0.3.0 (2025-10-11)
+v0.4.0 (2026-05-14)
+-------------------
+Contributor to this version: Baptiste Hamon (@baptistehamon).
+
+New features
+^^^^^^^^^^^^
+* ``SuitabilityCriteria`` now supports "inplace" computation, meaning that the suitability values are stored in the ``indicator`` attribute of the criteria (issue `#118 <https://github.com/baptistehamon/lsapy/issues/118>`_, PR `#123 <https://github.com/baptistehamon/lsapy/pull/123>`_).
+* LSAPy is now supports Python 3.14 (issue `#127 <https://github.com/baptistehamon/lsapy/issues/127>`_, PR `#128 <https://github.com/baptistehamon/lsapy/pull/128>`_).
+
+Bug fixes
+^^^^^^^^^
+* Fix ``lsapy.core.formatting.sc_repr`` function  to handle ``SuitabilityCriteria`` with non-empty ``xr.DataArray`` indicators and undefined ``func`` (issue `#115 <https://github.com/baptistehamon/lsapy/issues/115>`_, PR `#116 <https://github.com/baptistehamon/lsapy/pull/116>`_).
+* Fix ``lsapy.aggregate.aggregate`` function for ``mean`` and ``gmean`` aggregation when weights are provided (issue `#121 <https://github.com/baptistehamon/lsapy/issues/121>`_, PR `#122 <https://github.com/baptistehamon/lsapy/pull/122>`_).
+* Fix ``LandSuitabilityAnalysis.run`` to reassign attrs to each criteria in the return ``xr.Dataset`` (issue `#119 <https://github.com/baptistehamon/lsapy/issues/119>`_, PR `#124 <https://github.com/baptistehamon/lsapy/pull/124>`_).
+* Fix issue with ``open_data`` due to the release of the v2.0 of *NZGLID* (issue `#145 <https://github.com/baptistehamon/lsapy/issues/145>`_, PR `#146 <https://github.com/baptistehamon/lsapy/pull/146>`_).
+* Fix ``open_data`` list of supported variables printing and update docstring (issue `#143 <https://github.com/baptistehamon/lsapy/issues/143>`_, PR `#144 <https://github.com/baptistehamon/lsapy/pull/144>`_).
+* Update sample data hash in the registry file after *NZGLID* v2.0 modifications (PR `#149 <https://github.com/baptistehamon/lsapy/pull/149>`_).
+
+Breaking changes
+^^^^^^^^^^^^^^^^
+* The ``lsapy.functions`` module has been removed (PR `#104 <https://github.com/baptistehamon/lsapy/pull/104>`_).
+    * The ``SuitabilityFunction`` class has been removed.
+    * All the standardization functions contained in this module have been removed and are now only available in the ``lsapy.standardize`` module.
+    * The ``fit_membership`` function has been removed and ``lsapy.standardize.fit`` should be used instead.
+* The example data provided for the *land* realm with the package has been updated reflecting the changes in the v2.0 of *NZGLID* dataset (issue `#145 <https://github.com/baptistehamon/lsapy/issues/145>`_, PR `#146 <https://github.com/baptistehamon/lsapy/pull/146>`_):
+    * Minor changes in the data values have been introduced.
+    * The variable *rock* has been renamed to *rock_outcrops_surface_boulders*.
+    * The variable *carbon_content* has been removed.
+
+Internal changes
+^^^^^^^^^^^^^^^^
+* ``h5py`` has been added to the project dev dependencies (PR `#112 <https://github.com/baptistehamon/lsapy/pull/112>`_).
+* ``lsapy.aggregate._agg_weights`` has been modified to return a ``xr.DataArray`` where weights are distributed only along the ``variable`` dimension (issue `#117 <https://github.com/baptistehamon/lsapy/issues/117>`_, PR `#122 <https://github.com/baptistehamon/lsapy/pull/122>`_).
+* Dependabot has been configured to check version updates (issue `#129 <https://github.com/baptistehamon/lsapy/issues/129>`_, PR `#130 <https://github.com/baptistehamon/lsapy/pull/130>`_).
+* The registry file for example data has been updated and the DOIs have been set to the v2.0 of `NZGLID` (issue `#145 <https://github.com/baptistehamon/lsapy/issues/145>`_, PR `#146 <https://github.com/baptistehamon/lsapy/pull/146>`_).
+* ``_check_realm_vars`` test has been updated to unsure supported variables are correctly printed (issue `#143 <https://github.com/baptistehamon/lsapy/issues/143>`_, PR `#144 <https://github.com/baptistehamon/lsapy/pull/144>`_).
+* Update LSAPy description in the README file and documentation home page (PR `#151 <https://github.com/baptistehamon/lsapy/pull/151>`_).
+* The links to the development installation instructions have been added to the README and documentation (issue `#142 <https://github.com/baptistehamon/lsapy/issues/142>`_, PR `#151 <https://github.com/baptistehamon/lsapy/pull/151>`_).
+* Update the README file:
+    * A new section *Citation* has been added with the citation information of LSAPy (issue `#142 <https://github.com/baptistehamon/lsapy/issues/142>`_, PR `#151 <https://github.com/baptistehamon/lsapy/pull/151>`_).
+    * The *Quick Start* section has been split into two sections: *Quick install* and *Land Suitability Analysis (LSA)* (PR `#151 <https://github.com/baptistehamon/lsapy/pull/151>`_).
+
+v0.3.1 (2025-11-14)
+-------------------
+Contributor to this version: Baptiste Hamon (@baptistehamon).
+
+Bug fixes
+^^^^^^^^^
+* The `np.vectorize` decorator has been removed of standardization functions to fix fitting functions issues (issue `#101 <https://github.com/baptistehamon/lsapy/issues/101>`_, PR `#102 <https://github.com/baptistehamon/lsapy/pull/102>`_).
+
+v0.3.0 (2025-11-10)
 -------------------
 Contributor to this version: Baptiste Hamon (@baptistehamon).
 
 Announcements
 ^^^^^^^^^^^^^
-* `LSAPy` is now available on `conda-forge <https://anaconda.org/conda-forge/lsapy>`_ (issue `#68 <https://github.com/baptistehamon/lsapy/issues/68>`_, PR `#74 <https://github.com/baptistehamon/lsapy/pull/74>`_).
+* LSAPy is now available on `conda-forge <https://anaconda.org/conda-forge/lsapy>`_ (issue `#68 <https://github.com/baptistehamon/lsapy/issues/68>`_, PR `#74 <https://github.com/baptistehamon/lsapy/pull/74>`_).
 
 New features
 ^^^^^^^^^^^^
@@ -48,7 +98,7 @@ New features
 ^^^^^^^^^^^^
 * Functions' alternative names can now be used in ``SuitabilityFunction`` (PR `#43 <https://github.com/baptistehamon/lsapy/pull/43>`_).
 * The documentation of membership functions has been improved (PR `#43 <https://github.com/baptistehamon/lsapy/pull/43>`_).
-* `LSAPy` officially supports Python>=3.10 and is OS independent (PR `#46 <https://github.com/baptistehamon/lsapy/pull/46>`_).
+* LSAPy officially supports Python>=3.10 and is OS independent (PR `#46 <https://github.com/baptistehamon/lsapy/pull/46>`_).
 * ``repr`` methods of ``SuitabilityFunction``, ``SuitabilityCriteria`` and ``LandSuitabilityAnalysis`` have been modified to provide more user-friendly information (issue `#55 <https://github.com/baptistehamon/lsapy/issues/55>`_, PR `#59 <https://github.com/baptistehamon/lsapy/pull/59>`_).
 * A setter has been added to the ``attrs`` method of ``SuitabilityCriteria`` and ``LandSuitabilityAnalysis`` (issue `#55 <https://github.com/baptistehamon/lsapy/issues/55>`_, PR `#59 <https://github.com/baptistehamon/lsapy/pull/59>`_).
 * The ``open_data`` function has been added to the ``lsapy.utils`` module to load data from the LSAPy data repository (issue `#60 <https://github.com/baptistehamon/lsapy/issues/60>`_, PR `#62 <https://github.com/baptistehamon/lsapy/pull/62>`_).
@@ -68,7 +118,7 @@ Breaking changes
 
 Internal changes
 ^^^^^^^^^^^^^^^^
-* Tests have been added for currently implemented `LSAPy` functionalities (issue `#7 <https://github.com/baptistehamon/lsapy/issues/7>`_, PR `#46 <https://github.com/baptistehamon/lsapy/pull/46>`_).
+* Tests have been added for currently implemented LSAPy functionalities (issue `#7 <https://github.com/baptistehamon/lsapy/issues/7>`_, PR `#46 <https://github.com/baptistehamon/lsapy/pull/46>`_).
     * ``pytest`` is used as the testing framework to run all unit tests, doctests and test notebooks.
     * ``nox`` has been set up and is used to run tests in CI workflows.
 * A CI GitHub Actions workflow has been added (issue `#8 <https://github.com/baptistehamon/lsapy/issues/8>`_, PR `#46 <https://github.com/baptistehamon/lsapy/pull/46>`_)
@@ -81,17 +131,17 @@ Internal changes
     * Update package metadata: keywords, classifiers (python versions) and project URLs.
     * Update package sdist files.
 * The ``lsapy.core.formatting`` module has been added and contains ``repr`` formatting functions (issue `#55 <https://github.com/baptistehamon/lsapy/issues/55>`_, PR `#59 <https://github.com/baptistehamon/lsapy/pull/59>`_).
-* `LSAPy` sample data management has been improved (issue `#60 <https://github.com/baptistehamon/lsapy/issues/60>`_, PR `#62 <https://github.com/baptistehamon/lsapy/pull/62>`_):
-    * `LSAPy` now uses `pooch` to fetch sample data.
+* LSAPy sample data management has been improved (issue `#60 <https://github.com/baptistehamon/lsapy/issues/60>`_, PR `#62 <https://github.com/baptistehamon/lsapy/pull/62>`_):
+    * LSAPy now uses ``pooch`` to fetch sample data.
     * Old data files have been removed from the data folder, and the new climate data file has been added.
     * A registry file has been added to store sample data file names, hashes and URLs.
-* Aggregation functions have been moved to the `lsapy.core.aggregation` module (PR `#63 <https://github.com/baptistehamon/lsapy/pull/63>`_).
-* A relaxed configuration of `mypy` has been added to the project (PR `#66 <https://github.com/baptistehamon/lsapy/pull/66>`_).
+* Aggregation functions have been moved to the ``lsapy.core.aggregation`` module (PR `#63 <https://github.com/baptistehamon/lsapy/pull/63>`_).
+* A relaxed configuration of ``mypy`` has been added to the project (PR `#66 <https://github.com/baptistehamon/lsapy/pull/66>`_).
 
 Bug fixes
 ^^^^^^^^^
 * Fix issues with representations of ``SuitabilityFunction`` when no parameters are provided (issue `#61 <https://github.com/baptistehamon/lsapy/issues/61>`_, PR `#65 <https://github.com/baptistehamon/lsapy/pull/65>`_).
-* Add `**kwargs` to `SuitabilityCriteria.compute` and `LandSuitabilityAnalysis.run` to allow handling Dask arrays (issue `#64 <https://github.com/baptistehamon/lsapy/issues/64>`_, PR `#65 <https://github.com/baptistehamon/lsapy/pull/65>`_).
+* Add ``**kwargs`` to ``SuitabilityCriteria.compute`` and ``LandSuitabilityAnalysis.run`` to allow handling Dask arrays (issue `#64 <https://github.com/baptistehamon/lsapy/issues/64>`_, PR `#65 <https://github.com/baptistehamon/lsapy/pull/65>`_).
 * The codebase has been modified to improve typing and fix mypy errors (issue `#35 <https://github.com/baptistehamon/lsapy/issues/35>`_, PR `#66 <https://github.com/baptistehamon/lsapy/pull/66>`_).
 
 v0.1.1 (2025-07-26)
@@ -126,8 +176,8 @@ Internal changes
 * Templates for requesting new features, asking question and submitting PR have been added (issue `#11 <https://github.com/baptistehamon/lsapy/issues/11>`_, PR `#12 <https://github.com/baptistehamon/lsapy/pull/12>`_).
 * The README has been updated to make links permanent and to add a docs badge (PR `#13 <https://github.com/baptistehamon/lsapy/pull/13>`_).
 * A configuration file for Zenodo integration has been added to the repository (PR `#14 <https://github.com/baptistehamon/lsapy/pull/14>`_).
-* `Pre-commit` has been setup and `ruff`, `codespell` and `numpydoc` hooks have been added (issue `#8 <https://github.com/baptistehamon/lsapy/issues/8>`_, PR `#18 <https://github.com/baptistehamon/lsapy/pull/18>`_/PR `#19 <https://github.com/baptistehamon/lsapy/pull/19>`_).
-* The autoupdate schedule of `pre-commit` has been set to weekly (PR `#21 <https://github.com/baptistehamon/lsapy/pull/21>`_)
+* *Pre-commit* has been setup and ``ruff``, ``codespell`` and ``numpydoc`` hooks have been added (issue `#8 <https://github.com/baptistehamon/lsapy/issues/8>`_, PR `#18 <https://github.com/baptistehamon/lsapy/pull/18>`_/PR `#19 <https://github.com/baptistehamon/lsapy/pull/19>`_).
+* The autoupdate schedule of ``pre-commit`` has been set to weekly (PR `#21 <https://github.com/baptistehamon/lsapy/pull/21>`_)
 * The unused ``introduction.ipynb`` notebook has been removed (issue `#15 <https://github.com/baptistehamon/lsapy/issues/15>`_, PR `#20 <https://github.com/baptistehamon/lsapy/pull/20>`_).
 * The structure around ``SuitabilityFunction`` (PR `#30 <https://github.com/baptistehamon/lsapy/pull/30>`_):
     * The ``SuitabilityFunction`` has been moved to LSAPy ``function._suitability`` module.
@@ -148,7 +198,7 @@ Internal changes
 ^^^^^^^^^^^^^^^^
 * Major changes for documentation (issue `#2 <https://github.com/baptistehamon/lsapy/issues/2>`_, PR `#9 <https://github.com/baptistehamon/lsapy/pull/9>`_):
     * All public objects are now documented using the `NumPy-style <https://numpydoc.readthedocs.io/en/latest/format.html>`_.
-    * *introduction.ipynb* has been slip into three different ones: *criteria.ipynb*, *function.ipynb*, and *lsa.ipynb*.
+    * ``introduction.ipynb`` has been slip into three different ones: ``criteria.ipynb``, ``function.ipynb``, and ``lsa.ipynb``.
     * The top-level documentation has been updated/created:
         * The format of README and CHANGELOG files is now reStructuredText (RST).
         * A proper README has been created.
@@ -158,7 +208,7 @@ Internal changes
     * The documentation building using `Sphinx <https://www.sphinx-doc.org/en/master/>`_ has been setup:
         * The documentation uses the `PyData theme <https://pydata-sphinx-theme.readthedocs.io/en/stable/>`_.
         * A User-facing documentation is now available and has been published on `Read the Docs <https://readthedocs.org/>`_.
-    * The project dependencies have been updated and made consistent across *pyproject.toml* and *environments.yml* files.
+    * The project dependencies have been updated and made consistent across ``pyproject.toml`` and ``environments.yml`` files.
 
 v0.1.0-dev1 (2025-05-16)
 ------------------------

{lsapy-0.3.0 → lsapy-0.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: lsapy
-Version: 0.3.0
+Version: 0.4.0
 Summary: A Python package for Land Suitability Analysis.
 Keywords: LSAPy,Land Suitability Analysis,Geospatial Analysis,GIS,Geography
 Author-email: Baptiste Hamon <baptiste.hamon@pg.canterbury.ac.nz>
@@ -17,6 +17,7 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Classifier: Topic :: Scientific/Engineering :: GIS
 License-File: LICENSE
 Requires-Dist: geopandas >=0.14.0
@@ -34,6 +35,7 @@ Requires-Dist: codespell >=2.4.1 ; extra == "dev"
 Requires-Dist: coverage[toml] >=7.7.0 ; extra == "dev"
 Requires-Dist: flit >=3.11 ; extra == "dev"
 Requires-Dist: h5netcdf >=1.4.0 ; extra == "dev"
+Requires-Dist: h5py ; extra == "dev"
 Requires-Dist: ipython >=8.20.0 ; extra == "dev"
 Requires-Dist: matplotlib >=3.9.0 ; extra == "dev"
 Requires-Dist: mypy >=1.17.1 ; extra == "dev"
@@ -65,6 +67,10 @@ Provides-Extra: all
 Provides-Extra: dev
 Provides-Extra: docs
 
+==========================================
+LSAPy: Land Suitability Analysis in Python
+==========================================
+
 .. image:: https://raw.githubusercontent.com/baptistehamon/lsapy/main/docs/logos/lsapy/LSAPy_Logo_FullColour.png
     :class: dark-light
     :align: center
@@ -72,19 +78,26 @@ Provides-Extra: docs
     :width: 400px
     :alt: LSAPy Logo
 
-LSAPy: Land Suitability Analysis in Python
-==========================================
-|pypi| |conda| |python-versions| |status| |testing| |coverage| |ruff| |pre-commit| |docs| |question| |zenodo|
+|pypi| |conda| |python-versions| |status| |testing| |coverage| |ruff| |pre-commit| |docs| |question| |preprint| |zenodo|
+
+*LSAPy* (Land Suitability Analysis in Python) is a highly customizable, open-source Python library designed
+to streamline and enhance Land Suitability Analysis (LSA) workflows. Its objective is to make conducting LSA
+in Python easier and more accessible to users. The package implements a fuzzy-logic approach and provides a
+set of objects that work together to deliver a flexible and user-defined LSA framework.
 
-`LSAPy` stands for Land Suitability Analysis (LSA) in Python. Its objective is to make conducting
-LSA in Python easier and more accessible to users. It provides a set of objects built around
-`xarray`_ and operating together, making LSA's workflow straight forward and easy to understand.
+By relying on `xarray`_ objects for computation, *LSAPy* is specifically designed to facilitate LSA under climate
+change projections. Moreover, the use of `xarray`_ allows for seamless integration with the broader Python ecosystem,
+such as `dask`_ for efficient parallel processing and `matplotlib`_ for data visualisation. The modular design of
+*LSAPy* addresses some limitations of existing LSA tools by offering greater flexibility, reproducibility, and
+scalability for research and practical applications.
 
 .. _`xarray`: https://xarray.pydata.org/en/stable/
+.. _`dask`: https://docs.dask.org/en/stable/
+.. _`matplotlib`: https://matplotlib.org/stable/
 
-Quick Start
------------
-To install `LSAPy`, you can use `pip`:
+Quick Install
+-------------
+To install *LSAPy*, you can use `pip`:
 
 .. code-block:: shell
 
@@ -96,7 +109,14 @@ or `conda`:
 
     conda install -c conda-forge lsapy
 
-You can now perform your LSA:
+You can find the development installation instructions in the `Contribution`_ section.
+
+Land Suitability Analysis (LSA)
+-------------------------------
+
+Below is a quick example of how to conduct a land suitability analysis using *LSAPy*.
+
+.. _`User Guide`: https://lsapy.readthedocs.io/en/latest/notebooks/index.html
 
 .. code-block:: python
 
@@ -129,29 +149,36 @@ You can now perform your LSA:
     # run your analysis
     lsa.run(params)
 
-More detailed tutorials and examples can be found in the `User Guide`_.
-
-.. _`User Guide`: https://lsapy.readthedocs.io/en/latest/notebooks/index.html
-
+For more detailed tutorials and examples, please refer to the `User Guide`_.
 
 Contributing
 ------------
 
-`LSAPy` is an open-source project and we welcome contributions from the community. If you are interested in contributing, please
+*LSAPy* is an open-source project and we welcome contributions from the community. If you are interested in contributing, please
 refer to the `Contribution`_ section for guidelines on how to get started helping us improve the library.
 
-.. _`Contribution`: https://lsapy.readthedocs.io/en/latest/community/contributing.html
+How to cite *LSAPy*
+-------------------
+
+If you use *LSAPy* in your research or project, please consider citing it. The software is currently under review by
+`pyOpenSci <https://github.com/pyOpenSci/software-submission/issues/261>`__  for publication in the `Journal of Open Source Software`
+(JOSS), and we will update this section with the relevant reference once the review process is complete. In the meantime,
+you can cite the preprint, which is available on `Research Square` : https://doi.org/10.21203/rs.3.rs-8399348/v1.
+
+If you wish to cite a specific version of the software, you can find the relevant reference on `Zenodo` :
+https://doi.org/10.5281/zenodo.15015110.
 
 Credits
 -------
 
-The development of `LSAPy` started as part of a PhD, funded by the `Food Transition 2050`_  Joint Postgraduate School and hosted
+The development of *LSAPy* started as part of a PhD, funded by the `Food Transition 2050`_  Joint Postgraduate School and hosted
 by the `University of Canterbury`_ in New Zealand.
 
 |FT2050| |UC-white| |UC-black|
 
 The Python package has been created following the `pyOpenSci Guidebook`_.
 
+.. _`Contribution`: https://lsapy.readthedocs.io/en/latest/community/contributing.html
 .. _`Food Transition 2050`: https://www.foodtransitions2050.ac.nz/
 .. _`University of Canterbury`: https://www.canterbury.ac.nz/
 .. _`pyOpenSci Guidebook`: https://www.pyopensci.org/python-package-guide/
@@ -224,3 +251,7 @@ The Python package has been created following the `pyOpenSci Guidebook`_.
         :target: https://pypi.python.org/pypi/lsapy
         :alt: Supported Python Versions
 
+.. |preprint| image:: https://img.shields.io/badge/preprint-10.21203%2Frs.3.rs--8399348%2Fv1-brightgreen?style=flat&color=brightgreen
+    :target: https://doi.org/10.21203/rs.3.rs-8399348/v1
+    :alt: Link to preprint on Research Square
+

{lsapy-0.3.0 → lsapy-0.4.0}/README.rst

@@ -1,3 +1,7 @@
+==========================================
+LSAPy: Land Suitability Analysis in Python
+==========================================
+
 .. image:: https://raw.githubusercontent.com/baptistehamon/lsapy/main/docs/logos/lsapy/LSAPy_Logo_FullColour.png
     :class: dark-light
     :align: center
@@ -5,19 +9,26 @@
     :width: 400px
     :alt: LSAPy Logo
 
-LSAPy: Land Suitability Analysis in Python
-==========================================
-|pypi| |conda| |python-versions| |status| |testing| |coverage| |ruff| |pre-commit| |docs| |question| |zenodo|
+|pypi| |conda| |python-versions| |status| |testing| |coverage| |ruff| |pre-commit| |docs| |question| |preprint| |zenodo|
+
+*LSAPy* (Land Suitability Analysis in Python) is a highly customizable, open-source Python library designed
+to streamline and enhance Land Suitability Analysis (LSA) workflows. Its objective is to make conducting LSA
+in Python easier and more accessible to users. The package implements a fuzzy-logic approach and provides a
+set of objects that work together to deliver a flexible and user-defined LSA framework.
 
-`LSAPy` stands for Land Suitability Analysis (LSA) in Python. Its objective is to make conducting
-LSA in Python easier and more accessible to users. It provides a set of objects built around
-`xarray`_ and operating together, making LSA's workflow straight forward and easy to understand.
+By relying on `xarray`_ objects for computation, *LSAPy* is specifically designed to facilitate LSA under climate
+change projections. Moreover, the use of `xarray`_ allows for seamless integration with the broader Python ecosystem,
+such as `dask`_ for efficient parallel processing and `matplotlib`_ for data visualisation. The modular design of
+*LSAPy* addresses some limitations of existing LSA tools by offering greater flexibility, reproducibility, and
+scalability for research and practical applications.
 
 .. _`xarray`: https://xarray.pydata.org/en/stable/
+.. _`dask`: https://docs.dask.org/en/stable/
+.. _`matplotlib`: https://matplotlib.org/stable/
 
-Quick Start
------------
-To install `LSAPy`, you can use `pip`:
+Quick Install
+-------------
+To install *LSAPy*, you can use `pip`:
 
 .. code-block:: shell
 
@@ -29,7 +40,14 @@ or `conda`:
 
     conda install -c conda-forge lsapy
 
-You can now perform your LSA:
+You can find the development installation instructions in the `Contribution`_ section.
+
+Land Suitability Analysis (LSA)
+-------------------------------
+
+Below is a quick example of how to conduct a land suitability analysis using *LSAPy*.
+
+.. _`User Guide`: https://lsapy.readthedocs.io/en/latest/notebooks/index.html
 
 .. code-block:: python
 
@@ -62,29 +80,36 @@ You can now perform your LSA:
     # run your analysis
     lsa.run(params)
 
-More detailed tutorials and examples can be found in the `User Guide`_.
-
-.. _`User Guide`: https://lsapy.readthedocs.io/en/latest/notebooks/index.html
-
+For more detailed tutorials and examples, please refer to the `User Guide`_.
 
 Contributing
 ------------
 
-`LSAPy` is an open-source project and we welcome contributions from the community. If you are interested in contributing, please
+*LSAPy* is an open-source project and we welcome contributions from the community. If you are interested in contributing, please
 refer to the `Contribution`_ section for guidelines on how to get started helping us improve the library.
 
-.. _`Contribution`: https://lsapy.readthedocs.io/en/latest/community/contributing.html
+How to cite *LSAPy*
+-------------------
+
+If you use *LSAPy* in your research or project, please consider citing it. The software is currently under review by
+`pyOpenSci <https://github.com/pyOpenSci/software-submission/issues/261>`__  for publication in the `Journal of Open Source Software`
+(JOSS), and we will update this section with the relevant reference once the review process is complete. In the meantime,
+you can cite the preprint, which is available on `Research Square` : https://doi.org/10.21203/rs.3.rs-8399348/v1.
+
+If you wish to cite a specific version of the software, you can find the relevant reference on `Zenodo` :
+https://doi.org/10.5281/zenodo.15015110.
 
 Credits
 -------
 
-The development of `LSAPy` started as part of a PhD, funded by the `Food Transition 2050`_  Joint Postgraduate School and hosted
+The development of *LSAPy* started as part of a PhD, funded by the `Food Transition 2050`_  Joint Postgraduate School and hosted
 by the `University of Canterbury`_ in New Zealand.
 
 |FT2050| |UC-white| |UC-black|
 
 The Python package has been created following the `pyOpenSci Guidebook`_.
 
+.. _`Contribution`: https://lsapy.readthedocs.io/en/latest/community/contributing.html
 .. _`Food Transition 2050`: https://www.foodtransitions2050.ac.nz/
 .. _`University of Canterbury`: https://www.canterbury.ac.nz/
 .. _`pyOpenSci Guidebook`: https://www.pyopensci.org/python-package-guide/
@@ -156,3 +181,7 @@ The Python package has been created following the `pyOpenSci Guidebook`_.
 .. |python-versions| image:: https://img.shields.io/pypi/pyversions/lsapy
         :target: https://pypi.python.org/pypi/lsapy
         :alt: Supported Python Versions
+
+.. |preprint| image:: https://img.shields.io/badge/preprint-10.21203%2Frs.3.rs--8399348%2Fv1-brightgreen?style=flat&color=brightgreen
+    :target: https://doi.org/10.21203/rs.3.rs-8399348/v1
+    :alt: Link to preprint on Research Square

{lsapy-0.3.0 → lsapy-0.4.0}/docs/api.rst

@@ -12,4 +12,3 @@ This page provides an overview of all functions, modules, objects implemented in
    api/lsa
    api/stats
    api/utils
-   api/deprecated

{lsapy-0.3.0 → lsapy-0.4.0}/docs/getting_started/index.rst

@@ -5,6 +5,7 @@ Getting Started
 Installation
 ------------
 
+.. _`Contribution`: https://lsapy.readthedocs.io/en/latest/community/contributing.html
 .. _PyPI: https://pypi.org/project/laspy/
 .. _conda-forge: https://conda-forge.org/
 
@@ -20,6 +21,8 @@ or from `conda-forge`_ using `conda`:
 
    conda install -c conda-forge lsapy
 
+You can find the development installation instructions in the `Contribution`_ section.
+
 Land Suitability Analysis (LSA)
 -------------------------------
 

lsapy-0.4.0/docs/index.rst

@@ -0,0 +1,40 @@
+.. lsapy documentation master file, created by
+   sphinx-quickstart on Tue Apr 22 19:32:21 2025.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+:html_theme.sidebar_secondary.remove:
+
+===================
+LSAPy Documentation
+===================
+
+Description
+-----------
+
+`LSAPy` (Land Suitability Analysis in Python) is a highly customizable, open-source Python library designed
+to streamline and enhance Land Suitability Analysis (LSA) workflows. Its objective is to make conducting LSA
+in Python easier and more accessible to users. The package implements a fuzzy-logic approach and provides a
+set of objects that work together to deliver a flexible and user-defined LSA framework.
+
+By relying on `xarray`_ objects for computation, `LSAPy` is specifically designed to facilitate LSA under climate
+change projections. Moreover, the use of `xarray`_ allows for seamless integration with the broader Python ecosystem,
+such as `dask`_ for efficient parallel processing and `matplotlib`_ for data visualisation. The modular design of
+`LSAPy` addresses some limitations of existing LSA tools by offering greater flexibility, reproducibility, and
+scalability for research and practical applications.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Table of Contents:
+
+   About <readme>
+   Getting Started <getting_started/index>
+   User Guide <notebooks/index>
+   API Reference <api>
+   Community <community/index>
+
+.. toctree::
+   :titlesonly:
+
+   changelog
+   references

{lsapy-0.3.0 → lsapy-0.4.0}/docs/notebooks/criteria.ipynb

@@ -27,6 +27,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "import lsapy.standardize as lstd\n",
     "from lsapy import SuitabilityCriteria\n",
     "from lsapy.utils import open_data\n",
     "\n",
@@ -36,7 +37,7 @@
     "    name=\"potential_root_depth\",\n",
     "    long_name=\"Potential Rooting Depth Suitability\",\n",
     "    indicator=potential_rooting_depth,\n",
-    "    func=\"vetharaniam2022_eq5\",\n",
+    "    func=lstd.vetharaniam2022_eq5,\n",
     "    fparams={\"a\": -11.98, \"b\": 0.459},\n",
     ")"
    ]
@@ -87,7 +88,7 @@
     "    name=\"water_requirements\",\n",
     "    long_name=\"Annual Rainfall Requirement Suitability\",\n",
     "    indicator=prtot,\n",
-    "    func=\"vetharaniam2022_eq5\",\n",
+    "    func=lstd.vetharaniam2022_eq5,\n",
     "    fparams={\"a\": 0.876, \"b\": 1248},\n",
     ")"
    ]

{lsapy-0.3.0 → lsapy-0.4.0}/docs/notebooks/index.rst

@@ -11,6 +11,5 @@ and explaining how they operate together to perform Land Suitability Analysis (L
 .. toctree::
    :maxdepth: 2
 
-   functions
    criteria
    lsa

{lsapy-0.3.0 → lsapy-0.4.0}/docs/notebooks/lsa.ipynb

@@ -28,6 +28,7 @@
     "import matplotlib.pyplot as plt\n",
     "from xclim.indicators.atmos import precip_accumulation\n",
     "\n",
+    "import lsapy.standardize as lstd\n",
     "from lsapy import LandSuitabilityAnalysis, SuitabilityCriteria\n",
     "from lsapy.utils import open_data\n",
     "\n",
@@ -54,7 +55,7 @@
     "            weight=2,\n",
     "            category=\"soil\",\n",
     "            indicator=soil_data[\"potential_rooting_depth\"],\n",
-    "            func=\"vetharaniam2022_eq5\",\n",
+    "            func=lstd.vetharaniam2022_eq5,\n",
     "            fparams={\"a\": -11.98, \"b\": 0.459},\n",
     "        ),\n",
     "        \"drainage_class\": SuitabilityCriteria(\n",
@@ -63,7 +64,7 @@
     "            category=\"soil\",\n",
     "            long_name=\"Drainage Class Suitability\",\n",
     "            indicator=soil_data[\"drainage\"],\n",
-    "            func=\"discrete\",\n",
+    "            func=lstd.discrete,\n",
     "            fparams={\"rules\": {0: 0, 1: 0.1, 2: 0.5, 3: 0.9, 4: 1}},\n",
     "        ),\n",
     "        \"water_requirements\": SuitabilityCriteria(\n",
@@ -72,7 +73,7 @@
     "            category=\"climate\",\n",
     "            long_name=\"Annual Rainfall Requirement Suitability\",\n",
     "            indicator=precip_accumulation(pr, freq=\"YS\"),\n",
-    "            func=\"vetharaniam2022_eq5\",\n",
+    "            func=lstd.vetharaniam2022_eq5,\n",
     "            fparams={\"a\": 0.876, \"b\": 1248},\n",
     "        ),\n",
     "    },\n",

{lsapy-0.3.0 → lsapy-0.4.0}/environment.yml

@@ -2,7 +2,7 @@ name: lsapy
 channels:
   - conda-forge
 dependencies:
-  - python >=3.10
+  - python >=3.10,<3.15
   - geopandas >=0.14.0
   - numpy >=1.26.0
   - pandas >=2.2.0
@@ -19,6 +19,7 @@ dependencies:
   - deptry >=0.23.0
   - flit >=3.11
   - h5netcdf >=1.4.0
+  - h5py
   - ipykernel
   - ipython >=8.20.0
   - matplotlib >=3.9.0

{lsapy-0.3.0 → lsapy-0.4.0}/noxfile.py

@@ -6,7 +6,7 @@ import nox
 nox.options.sessions = ("tests", "notebooks", "doctests")
 
 
-@nox.session(python=["3.10", "3.11", "3.12", "3.13"])
+@nox.session(python=["3.10", "3.11", "3.12", "3.13", "3.14"])
 def tests(session):
     session.install(".[dev]", "h5netcdf", "netCDF4")
     session.run("pytest")

{lsapy-0.3.0 → lsapy-0.4.0}/pyproject.toml

@@ -25,6 +25,7 @@ classifiers = [
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
     "Topic :: Scientific/Engineering :: GIS",
 ]
 dynamic = ["description", "version"]
@@ -47,6 +48,7 @@ dev = [
   "coverage[toml] >=7.7.0",
   "flit >=3.11",
   "h5netcdf >=1.4.0",
+  "h5py",
   "ipython >=8.20.0",
   "matplotlib >=3.9.0",
   "mypy >=1.17.1",
@@ -83,7 +85,7 @@ Issues = "https://github.com/baptistehamon/lsapy/issues"
 Zenodo = "https://doi.org/10.5281/zenodo.15015110"
 
 [tool.bumpversion]
-current_version = "0.3.0"
+current_version = "0.4.0"
 commit = true
 commit_args = "--no-verify --signoff"
 tag = false
@@ -227,6 +229,7 @@ ignore = [
 "docs/*.py" = ["D100", "D101", "D102", "D103", "PLR6301"]
 "src/lsapy/**/__init__.py" = ["F401", "F403"]
 "tests/**/test*.py" = ["D101", "D102", "D103", "PLR2004", "PLR6301", "S101"]
+"tests/**/conftest.py" = ["S101"]
 
 [tool.ruff.lint.isort]
 case-sensitive = true

{lsapy-0.3.0 → lsapy-0.4.0}/src/lsapy/__init__.py

@@ -1,9 +1,8 @@
 """A Python package for Land Suitability Analysis."""
 
 from lsapy.criteria import SuitabilityCriteria
-from lsapy.functions import *
 from lsapy.lsa import LandSuitabilityAnalysis
 
 __author__ = "Baptiste Hamon"
 __email__ = "baptiste.hamon@pg.canterbury.ac.nz"
-__version__ = "0.3.0"
+__version__ = "0.4.0"