chore: release 1.2.1 (#96)

.github/workflows/ci.yml

@@ -38,7 +38,7 @@ jobs:
         run: poetry --version
 
       - name: Install Project Dependencies
-        run: python -m poetry install
+        run: python -m poetry install --with dev
 
       - name: Lint Codebase with flake8
         run: |

CODE_OF_CONDUCT.md

@@ -0,0 +1,134 @@
+
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+[niclasrieger@gmail.com](mailto:niclasrieger@gmail.com).
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
+[https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations
+

README.rst

@@ -58,22 +58,21 @@
 Overview
 ---------------------
 
-``xeofs`` is a Python toolbox designed for methods like **Empirical Orthogonal Function (EOF) analysis**, also known as Principal Component Analysis (PCA), 
-and **related variants**. The package stands out due to its capacity 
-to handle multi-dimensional Earth observation data. 
+``xeofs`` is a dedicated Python package for dimensionality reduction in the realm of climate science, 
+offering methods like PCA, known as EOF analysis within the field, and related variants. 
+Seamlessly integrated with ``xarray`` and ``Dask``, it's tailored for easy handling and scalable 
+computation on large, multi-dimensional datasets, making advanced climate data analysis both accessible and efficient.
 
-Here are the key strengths of ``xeofs``:
+- **Multi-Dimensional**: Designed for ``xarray`` objects, it applies dimensionality reduction to multi-dimensional data while maintaining data labels.
+- **Dask-Integrated**: Supports large datasets via ``Dask`` xarray objects
+- **Extensive Methods**: Offers various dimensionality reduction techniques
+- **Adaptable Output**: Provides output corresponding to the type of input, whether single or list of ``xr.DataArray`` or ``xr.Dataset``
+- **Missing Values**: Handles ``NaN`` values within the data
+- **Bootstrapping**: Comes with a user-friendly interface for model evaluation using bootstrapping
+- **Efficient**: Ensures computational efficiency, particularly with large datasets through randomized SVD
+- **Modular**: Allows users to implement and incorporate new dimensionality reduction methods
 
-- **Multi-dimensional Analysis**: Execute labeled EOF analysis with the extensive features of ``xarray``.
-- **Scalability**: Handle large datasets effectively with ``dask``.
-- **Speed**: Enjoy quick EOF analysis using ``scipy``'s randomized SVD.
-- **Variety of Methods**: Perform diverse variants of EOF analysis, including **complex and rotated EOF analysis**, along with related techniques such as **Maximum Covariance Analysis (MCA)**.
-- **Model Validation**: Validate models through bootstrapping.
-- **Modular Code Structure**: Incorporate new EOF variants with ease due to the package's modular structure.
-- **Flexible Data Formats**: Accepts a variety of ``xarray`` input types (``DataArray``, ``Dataset``, list of ``DataArray``).
 
-Compared to similar packages like eofs_, pyEOF_, and xMCA_, ``xeofs`` is more comprehensive and flexible, providing unique capabilities like handling fully multidimensional dimensions 
-(both samples and features) and a simple interface for bootstrapping. This makes ``xeofs`` a powerful one-stop-shop for most of your EOF analysis needs.
 
 .. _pyEOF: https://github.com/zhonghua-zheng/pyEOF
 .. _xMCA: https://github.com/Yefee/xMCA
@@ -142,10 +141,10 @@ In order to get started with ``xeofs``, follow these simple steps:
    rot_scores = rotator.scores()  # Rotated expansion coefficients (temporal patterns)
 
 
-To further explore the capabilities of ``xeofs``, check the available documentation_ and examples_.
-For a full list of currently available methods, see the methods_ section.
+To further explore the capabilities of ``xeofs``, check out the available documentation_ and examples_.
+For a full list of currently available methods, see the `Reference API`_.
 
-.. _methods: https://xeofs.readthedocs.io/en/latest/models.html
+.. _`Reference API`: https://xeofs.readthedocs.io/en/latest/api.html
 
 
 
@@ -157,12 +156,13 @@ For a more comprehensive overview and usage examples, visit the documentation_.
 Contributing
 ------------
 
-Contributions are highly welcomed and appreciated. If you're interested in improving ``xeofs`` or fixing issues, please open a Github issue_.
+Contributions are highly welcomed and appreciated. If you're interested in improving ``xeofs`` or fixing issues, please read our 
+`Contributing Guide`_.
 
 License
 -------
 
-This project is licensed under the terms of the MIT license.
+This project is licensed under the terms of the MIT_ license.
 
 Contact
 -------
@@ -172,31 +172,31 @@ For questions or support, please open a Github issue_.
 
 
 .. _issue: https://github.com/nicrie/xeofs/issues
+.. _`Contributing Guide`: https://xeofs.readthedocs.io/en/latest/overview_3_contributing.html
 .. _documentation: https://xeofs.readthedocs.io/en/latest/
 .. _examples: https://xeofs.readthedocs.io/en/latest/auto_examples/index.html
-
+.. _MIT: https://github.com/nicrie/xeofs/blob/main/LICENSE
 
 
 Credits
 ----------------------
 
-I want to acknowledge
-
-- Andrew Dawson_, for his foundational Python package for EOF analysis.
-- Yefee_, whose work provided useful references for implementing MCA in ``xeofs``.
-- James Chapman_, creator of a Python package for Canonical Correlation Analysis.
-- Diego Bueso_, for his open-source ROCK-PCA implementation in Matlab.
-- The developers of NumPy_, pandas_, and xarray_ for their indispensable tools for scientific computations in Python.
+- Randomized PCA: scikit-learn_
+- EOF analysis: Python package eofs_ by Andrew Dawson
+- MCA: Python package xMCA_ by Yefee
+- CCA: Python package CCA-Zoo_ by James Chapman
+- ROCK-PCA: Matlab implementation by Diego Bueso_
 
 
 
 .. _NumPy: https://www.numpy.org
 .. _pandas: https://pandas.pydata.org
 .. _xarray: https://xarray.pydata.org
-.. _Chapman: https://github.com/jameschapman19/cca_zoo
+.. _scikit-learn: https://scikit-learn.org/stable/
+.. _CCA-Zoo: https://github.com/jameschapman19/cca_zoo
 .. _Bueso: https://github.com/DiegoBueso/ROCK-PCA
-.. _Dawson: https://github.com/ajdawson/eofs
-.. _Yefee: https://github.com/Yefee/xMCA
+.. _eofs: https://github.com/ajdawson/eofs
+.. _xMCA: https://github.com/Yefee/xMCA
 
 
 How to cite?

docs/_autosummary/xeofs.models.CCA.rst

@@ -0,0 +1,39 @@
+xeofs.models.CCA
+================
+
+.. currentmodule:: xeofs.models
+
+.. autoclass:: CCA
+   :members:
+   :show-inheritance: 
+   :inherited-members:
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~CCA.__init__
+      ~CCA.components
+      ~CCA.explained_covariance
+      ~CCA.explained_covariance_ratio
+      ~CCA.explained_variance
+      ~CCA.explained_variance_ratio
+      ~CCA.fit
+      ~CCA.get_metadata_routing
+      ~CCA.get_params
+      ~CCA.scores
+      ~CCA.set_fit_request
+      ~CCA.set_params
+      ~CCA.set_transform_request
+      ~CCA.transform
+      ~CCA.weights
+
+
+
+
+
+

docs/_autosummary/xeofs.models.ExtendedEOF.rst

@@ -0,0 +1,36 @@
+xeofs.models.ExtendedEOF
+========================
+
+.. currentmodule:: xeofs.models
+
+.. autoclass:: ExtendedEOF
+   :members:
+   :show-inheritance: 
+   :inherited-members:
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~ExtendedEOF.__init__
+      ~ExtendedEOF.components
+      ~ExtendedEOF.compute
+      ~ExtendedEOF.explained_variance
+      ~ExtendedEOF.explained_variance_ratio
+      ~ExtendedEOF.fit
+      ~ExtendedEOF.fit_transform
+      ~ExtendedEOF.get_params
+      ~ExtendedEOF.inverse_transform
+      ~ExtendedEOF.scores
+      ~ExtendedEOF.singular_values
+      ~ExtendedEOF.transform
+
+
+
+
+
+

docs/_autosummary/xeofs.models.GWPCA.rst

@@ -0,0 +1,36 @@
+xeofs.models.GWPCA
+==================
+
+.. currentmodule:: xeofs.models
+
+.. autoclass:: GWPCA
+   :members:
+   :show-inheritance: 
+   :inherited-members:
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~GWPCA.__init__
+      ~GWPCA.components
+      ~GWPCA.compute
+      ~GWPCA.explained_variance
+      ~GWPCA.explained_variance_ratio
+      ~GWPCA.fit
+      ~GWPCA.fit_transform
+      ~GWPCA.get_params
+      ~GWPCA.inverse_transform
+      ~GWPCA.largest_locally_weighted_components
+      ~GWPCA.scores
+      ~GWPCA.transform
+
+
+
+
+
+