Merge pull request #98 from wilsonrljr/v0.3.0

V0.3.0

Author: wilsonrljr

.github/workflows/python-package.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
 
     steps:
     - uses: actions/checkout@v2
@@ -27,7 +27,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install flake8 pytest pytest-cov scikit-learn black isort>=5.0.6
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        if [ -f requirements.txt ]; then pip install .["dev"]; fi
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names

CHANGELOG

@@ -5,37 +5,71 @@ File for tracking changes in SysIdentPy
 Changes in SysIdentPy
 =====================
 
-v0.2.2
+v0.3.0
 ------
 
 CONTRIBUTORS
 ~~~~~~~~~~~~
 
 - wilsonrljr
+- gamcorn
+- Gabo-Tor
 
 CHANGES
 ~~~~~~~
 
-- The update **v0.2.2**  has been released with additional feature, minor API changes and fixes. 
+- The update **v0.3.0**  has been released with additional features, API changes and fixes. 
 
 - MAJOR: Estimators support in AOLS
-- MAJOR: 
-    - Refactored base class for model structure selection.
+    - Now you can use any SysIdentPy estimator in AOLS model structure selection. 
+
+- API Change: 
+    - Refactored base class for model structure selection. A refactored base class for model structure selection has been introduced in SysIdentPy. This update aims to enhance the system identification process by preparing the package for new features that are currently in development, like multiobjective parameter estimation, new basis functions and more.
+
+    Several methods within the base class have undergone significant restructuring to improve their functionality and optimize their performance. This reorganization will facilitate the incorporation of advanced model selection techniques in the future, which will enable users to obtain dynamic models with robust dynamic and static performance.
     - Avoid unnecessary inheritance in every MSS method and improve the readability with better structured classes.
     - Rewritten methods to avoid code duplication.
     - Improve overall code readability by rewriting if/elif/else clauses.
 
+- Breaking Change: `X_train` and `y_train` were replaced respectively by `X` and `y` in `fit` method in MetaMSS model structure selection algorithm.  `X_test` and `y_test` were replaced by `X` and `y` in `predict` method in MetaMSS.
+
+- API Change: Added BaseBasisFunction class, an abstract base class for implementing basis functions. 
+
+- Enhancement: Added support for python 3.11.
+
+- Future Deprecation Warning: The user will have to define the estimator and pass it to every model structure selection algorithm instead of using a string to define the Estimator. Currently the estimator is defined like "estimator='least_squares'". In version 0.4.0 the definition will be like "estimator=LeastSquares()"
+
+- FIX: Issue #96. Fix issue with numpy 1.24.* version. Thanks for the contribution @gamcorn.
+
+- FIX: Issue #91. Fix r2_score metric issue with 2 dimensional arrays.
+
+- FIX: Issue #90.
+
+- FIX: Issue #88 .Fix one step ahead prediction error in SimulateNARMAX class (thanks for pointing out, Lalith).
+
 - FIX: Fix error in selecting the correct regressors in AOLS.
-- FIX: Fix one step ahead prediction error in SimulateNARMAX class (thanks Lalith).
+
 - Fix: Fix n step ahead prediction method not returning all values of the defined steps-ahead value when passing only the initial condition.
+
 - FIX: Fix Visible Deprecation Warning raised in get_max_lag method.
+
 - FIX: Fix deprecation warning in Extended Least Squares Example
+
 - DATASET: Added air passengers dataset to SysIdentPy repository. 
+
 - DATASET: Added San Francisco Hospital Load dataset to SysIdentPy repository. 
+
 - DATASET: Added San Francisco PV GHI dataset to SysIdentPy repository.
+
 - DOC: Improved documentation in Setting Specif Lags page. Now we bring an example of how to set specific lags for MISO models.
+
 - DOC: Minor additions and grammar fixes.
 
+- DOC: Improve image visualization using mkdocs-glightbox.
+
+- Update dev packages versions
+
+
 v0.2.1
 ------
 

CONTRIBUTING.md

@@ -0,0 +1,236 @@
+---
+template: overrides/main.html
+title: Contribute
+---
+
+# Contributing
+
+SysIdentPy is intended to be a community project, hence all contributions are welcome! There exist many possible use cases in System Identification field and we can not test all scenarios without your help! If you find any bugs or have suggestions, please report them on [issue tracker] on GitHub.
+
+>We welcome new contributors of all experience levels. The SysIdentPy community goals are to be helpful, welcoming, and effective.
+
+  [issue tracker]: https://github.com/wilsonrljr/sysidentpy/issues
+
+## Help others with issues in GitHub
+
+You can see <a href="https://github.com/wilsonrljr/sysidentpy/issues" class="external-link" target="_blank">existing issues</a> and try and help others, most of the times they are questions that you might already know the answer for.
+
+## Watch the GitHub repository
+
+You can [watch] SysIdentPy in GitHub (clicking the "watch" button at the top right):
+  [watch]: https://github.com/wilsonrljr/sysidentpy
+
+If you select "Watching" instead of "Releases only" you will receive notifications when someone creates a new issue.
+
+Then you can try and help them solve those issues.
+
+## Documentation
+
+Documentation is as important as the library itself. English is not the primary language of the main authors, so if you find any typo or anything wrong do not hesitate to point out to us.
+
+## Create a Pull Request
+
+You can [contribute](contribute.md){.internal-link target=_blank} to the source code with Pull Requests, for example:
+
+* To fix a typo you found on the documentation.
+* To share an article, video, or podcast you created or found about SysIdentPy.
+* To propose new documentation sections.
+* To fix an existing issue/bug.
+* To add a new feature.
+
+## Development environment
+
+These are some basic steps to help us with code:
+
+- [x]	Install and Setup Git on your computer.
+- [x]	[Fork] SysIdentPy.
+- [x]	[Clone] the fork on your local machine.
+- [x]	Create a new branch.
+- [x]	Make changes following the coding style of the project (or suggesting improvements).
+- [x]	Run the tests.
+- [x]	Write and/or adapt existing test if needed.
+- [x]	Add documentation if needed.
+- [x]	Commit.
+- [x]	[Push] to your fork.
+- [x]	Open a [pull_request].
+
+  [Fork]: https://help.github.com/articles/fork-a-repo/
+  [Clone]: https://help.github.com/articles/cloning-a-repository/
+  [Push]: https://help.github.com/articles/pushing-to-a-remote/
+  [pull_request]: https://help.github.com/articles/creating-a-pull-request/
+
+
+### Environment
+
+Clone the repository using
+
+```console
+git clone https://github.com/wilsonrljr/sysidentpy.git
+```
+
+If you already cloned the repository and you know that you need to deep dive in the code, here are some guidelines to set up your environment.
+
+#### Virtual environment with `venv`
+
+You can create a virtual environment in a directory using Python's `venv` module or Conda:
+
+=== "venv"
+
+    ```console
+    $ python -m venv env
+    ```
+
+=== "conda"
+
+    ```console
+    conda create -n env
+    ```
+
+
+That will create a directory `./env/` with the Python binaries and then you will be able to install packages for that isolated environment.
+
+#### Activate the environment
+
+If you created the environment using Python's `venv` module, activate it with:
+
+=== "Linux, macOS"
+
+    ```console
+    source ./env/bin/activate
+    ```
+
+=== "Windows PowerShell"
+
+    ```console
+    .\env\Scripts\Activate.ps1
+    ```
+
+=== "Windows Bash"
+
+    Or if you use Bash for Windows (e.g. <a href="https://gitforwindows.org/" class="external-link" target="_blank">Git Bash</a>):
+
+    ```console
+    source ./env/Scripts/activate
+    ```
+
+If you created the environment using Conda, activate it with:
+
+=== "Conda Bash"
+
+    Or if you use Bash for Windows (e.g. <a href="https://gitforwindows.org/" class="external-link" target="_blank">Git Bash</a>):
+
+    ```console
+    conda activate env
+    ```
+
+To check it worked, use:
+
+=== "Linux, macOS, Windows Bash"
+
+    ```console
+    $ which pip
+
+    some/directory/sysidentpy/env/Scripts/pip
+    ```
+
+=== "Windows PowerShell"
+
+    ```console
+    $ Get-Command pip
+
+    some/directory/sysidentpy/env/Scripts/pip
+    ```
+
+=== "Windows Bash"
+
+    ```console
+    $ where pip
+
+    some/directory/sysidentpy/env/Scripts/pip
+    ```
+
+If it shows the `pip` binary at `env/bin/pip` then it worked.
+
+
+
+!!! tip
+    Every time you install a new package with `pip` under that environment, activate the environment again.
+
+
+
+!!! note
+	We use the `pytest` package for testing. The test functions are located in tests subdirectories at each folder inside SysIdentPy, which check the validity of the algorithms.
+
+#### Dependencies
+
+Install SysIdentPy with the `dev` and `docs` option to get all the necessary dependencies to run the tests
+
+=== "Dev and Docs dependencies"
+
+    ``` sh
+    pip install "sysidentpy[dev, docs]"
+    ```
+
+## Docs
+
+First, make sure you set up your environment as described above, that will install all the requirements.
+
+The documentation uses <a href="https://www.mkdocs.org/" class="external-link" target="_blank">MkDocs</a> and <a href="https://squidfunk.github.io/mkdocs-material/" class="external-link" target="_blank">Material for MKDocs</a>.
+
+All the documentation is in Markdown format in the directory `./docs/`.
+
+### Check the changes
+
+During local development, you can serve the website locally and checks for any changes. This helps making sure that:
+
+* All of your modifications were applied.
+* The unmodified files are displaying as expected.
+
+
+```console
+$ mkdocs serve
+
+INFO     -  [13:25:00] Browser connected: http://127.0.0.1:8000
+```
+
+It will serve the documentation on `http://127.0.0.1:8008`.
+
+That way, you can keep editing the source files and see the changes live.
+
+!!! warning
+  If any modification break the build, you have to serve the website again. Always check your `console` to make sure you are serving the website.
+
+
+## Run tests locally
+
+Its always good to check if your implementations/modifications does not break any other part of the package. You can run the SysIdentPy tests locally using `pytest` in the respective folder to perform all the tests of the corresponding sub-packages.
+
+#### Example of how to run the tests:
+
+Open a terminal emulator of your choice and go to a subdirectory, e.g,
+
+	\sysidentpy\metrics\
+
+Just type `pytest` in the terminal emulator
+
+```console
+pytest
+```
+
+and you get a result like:
+
+```console
+========== test session starts ==========
+
+platform linux -- Python 3.7.6, pytest-5.4.2, py-1.8.1, pluggy-0.13.1
+
+rootdir: ~/sysidentpy
+
+plugins: cov-2.8.1
+
+collected 12 items
+
+tests/test_regression.py ............ [100%]
+
+========== 12 passed in 2.45s ==================
+```