Merge pull request #408 from zStupan/update-docs

update docs

.github/dependabot.yml

@@ -0,0 +1,12 @@
+version: 2
+
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "monthly"

.readthedocs.yml

@@ -1,5 +1,25 @@
-requirements_file: docs/requirements.txt
+# Read the Docs configuration file for Sphinx projects
+# 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:
-  image: latest
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+
+sphinx:
+  configuration: docs/source/conf.py
+  fail_on_warning: true
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: all
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
 python:
-  version: 3.9
+  install:
+    - requirements: docs/requirements.txt

README.md

@@ -4,23 +4,17 @@
 
 
 
-![Check codestyle and test build](https://github.com/NiaOrg/NiaPy/workflows/Check%20and%20Test/badge.svg)
+![Check codestyle and test build](https://github.com/NiaOrg/NiaPy/actions/workflows/main.yml/badge.svg)
 [![PyPI Version](https://img.shields.io/pypi/v/NiaPy.svg)](https://pypi.python.org/pypi/NiaPy)
-![PyPI - Python Version](https://img.shields.io/pypi/pyversions/NiaPy.svg)
 ![PyPI - Status](https://img.shields.io/pypi/status/NiaPy.svg)
 ![PyPI - Downloads](https://img.shields.io/pypi/dm/NiaPy.svg)
-[![Downloads](https://pepy.tech/badge/niapy)](https://pepy.tech/project/niapy)
-![GitHub Release Date](https://img.shields.io/github/release-date/NiaOrg/NiaPy.svg)
-[![Anaconda-Server Badge](https://anaconda.org/niaorg/niapy/badges/installer/conda.svg)](https://conda.anaconda.org/niaorg)
+[![Anaconda Badge](https://anaconda.org/niaorg/niapy/badges/version.svg)](https://conda.anaconda.org/niaorg)
 [![Fedora package](https://img.shields.io/fedora/v/python3-niapy?color=blue&label=Fedora%20Linux&logo=fedora)](https://src.fedoraproject.org/rpms/python-niapy)
 [![AUR package](https://img.shields.io/aur/version/python-niapy?color=blue&label=Arch%20Linux&logo=arch-linux)](https://aur.archlinux.org/packages/python-niapy)
 [![Documentation Status](https://readthedocs.org/projects/niapy/badge/?version=latest)](http://niapy.readthedocs.io/en/latest/?badge=latest)
 [![GitHub license](https://img.shields.io/github/license/NiaOrg/NiaPy.svg)](https://github.com/NiaOrg/NiaPy/blob/master/LICENSE)
 
-[![Scrutinizer Code Quality](https://scrutinizer-ci.com/g/NiaOrg/NiaPy/badges/quality-score.png?b=master)](https://scrutinizer-ci.com/g/NiaOrg/NiaPy/?branch=master)
-[![Coverage Status](https://img.shields.io/coveralls/NiaOrg/NiaPy/master.svg)](https://coveralls.io/r/NiaOrg/NiaPy)
 ![GitHub commit activity](https://img.shields.io/github/commit-activity/w/NiaOrg/NiaPy.svg)
-[![Updates](https://pyup.io/repos/github/NiaOrg/NiaPy/shield.svg)](https://pyup.io/repos/github/NiaOrg/NiaPy/)
 [![Average time to resolve an issue](http://isitmaintained.com/badge/resolution/NiaOrg/NiaPy.svg)](http://isitmaintained.com/project/NiaOrg/NiaPy "Average time to resolve an issue")
 [![Percentage of issues still open](http://isitmaintained.com/badge/open/NiaOrg/NiaPy.svg)](http://isitmaintained.com/project/NiaOrg/NiaPy "Percentage of issues still open")
 ![GitHub contributors](https://img.shields.io/github/contributors/NiaOrg/NiaPy.svg)
@@ -33,7 +27,7 @@ Nature-inspired algorithms are a very popular tool for solving optimization prob
 
 * **Free software:** MIT license
 * **Documentation:** https://niapy.readthedocs.io/en/stable/
-* **Python versions:** 3.9.x, 3.10.x, 3.11.x
+* **Python versions:** 3.9.x, 3.10.x, 3.11.x, 3.12.x
 * **Dependencies:** [click here](CONTRIBUTING.md#development-dependencies)
 
 # Mission
@@ -51,52 +45,51 @@ Our mission is to build a collection of nature-inspired algorithms and create a
 Install NiaPy with pip:
 
 ```sh
-$ pip install niapy
+pip install niapy
 ```
 
 To install NiaPy with conda, use:
 
 ```sh
-$ conda install -c niaorg niapy
+conda install -c niaorg niapy
 ```
 
 To install NiaPy on Fedora, use:
 
 ```sh
-$ dnf install python3-niapy
+dnf install python3-niapy
 ```
 
 To install NiaPy on Arch Linux, please use an [AUR helper](https://wiki.archlinux.org/title/AUR_helpers):
 
 ```sh
-$ yay -Syyu python-niapy
+yay -Syyu python-niapy
 ```
 
 To install NiaPy on Alpine Linux, please enable Community repository and use:
 
 ```sh
-$ apk add py3-niapy
+apk add py3-niapy
 ```
 
 To install NiaPy on NixOS, please use:
 
 ```sh
-$ nix-env -iA nixos.python310Packages.niapy
+nix-env -iA nixos.python310Packages.niapy
 ```
 
 To install NiaPy on Void Linux, use:
 
 ```sh
-$ xbps-install -S python3-niapy
+xbps-install -S python3-niapy
 ```
 
 ## Install from source
 
 In case you want to install directly from the source code, use:
 
 ```sh
-$ git clone https://github.com/NiaOrg/NiaPy.git
-$ pip install NiaPy/
+pip install git+https://github.com/NiaOrg/NiaPy.git
 ```
 
 # Algorithms
@@ -309,8 +302,6 @@ This project follows the [all-contributors](https://github.com/all-contributors/
 
 ## Contributing
 
-[![Open Source Helpers](https://www.codetriage.com/niaorg/niapy/badges/users.svg)](https://www.codetriage.com/niaorg/niapy)
-
 We encourage you to contribute to NiaPy! Please check out the [Contributing to NiaPy guide](CONTRIBUTING.md) for guidelines about how to proceed.
 
 Everyone interacting in NiaPy's codebases, issue trackers, chat rooms and mailing lists is expected to follow the NiaPy [code of conduct](CODE_OF_CONDUCT.md).

docs/requirements.txt

@@ -1,26 +1,62 @@
-alabaster>=0.7.10
-Babel>=2.5.3
-certifi>=2018.1.18
-chardet>=3.0.4
-docutils>=0.14
-idna>=2.6
-imagesize>=1.0.0
-Jinja2>=2.10
-MarkupSafe>=1.0
-packaging>=16.8
-Pygments>=2.2.0
-pyparsing>=2.2.0
-pytz>=2018.3
-requests>=2.18.4
-six>=1.11.0
-snowballstemmer>=1.2.1
-sphinx>=1.8.5
-#sphinx-rtd-theme>=0.2.4
-sphinx-press-theme>=0.5.1
-sphinxcontrib-napoleon>=0.7
-sphinxcontrib-websupport>=1.0.1
-urllib3>=1.22
-xlsxWriter>=1.1.5
-numpy>=1.16.2
-scipy>=1.2.1
-matplotlib>=3.0.2
+#
+# This file is autogenerated by pip-compile with Python 3.11
+# by the following command:
+#
+#    pip-compile requirements.in
+#
+alabaster==0.7.13
+    # via sphinx
+babel==2.13.1
+    # via sphinx
+certifi==2023.7.22
+    # via requests
+charset-normalizer==3.3.1
+    # via requests
+docutils==0.18.1
+    # via
+    #   sphinx
+    #   sphinx-rtd-theme
+idna==3.4
+    # via requests
+imagesize==1.4.1
+    # via sphinx
+jinja2==3.1.2
+    # via sphinx
+markupsafe==2.1.3
+    # via jinja2
+packaging==23.2
+    # via sphinx
+pygments==2.16.1
+    # via sphinx
+requests==2.31.0
+    # via sphinx
+snowballstemmer==2.2.0
+    # via sphinx
+sphinx==7.2.6
+    # via
+    #   -r requirements.in
+    #   sphinx-rtd-theme
+    #   sphinxcontrib-applehelp
+    #   sphinxcontrib-devhelp
+    #   sphinxcontrib-htmlhelp
+    #   sphinxcontrib-jquery
+    #   sphinxcontrib-qthelp
+    #   sphinxcontrib-serializinghtml
+sphinx-rtd-theme==1.3.0
+    # via -r requirements.in
+sphinxcontrib-applehelp==1.0.7
+    # via sphinx
+sphinxcontrib-devhelp==1.0.5
+    # via sphinx
+sphinxcontrib-htmlhelp==2.0.4
+    # via sphinx
+sphinxcontrib-jquery==4.1
+    # via sphinx-rtd-theme
+sphinxcontrib-jsmath==1.0.1
+    # via sphinx
+sphinxcontrib-qthelp==1.0.6
+    # via sphinx
+sphinxcontrib-serializinghtml==1.1.9
+    # via sphinx
+urllib3==2.0.7
+    # via requests

docs/source/api/niapy.rst

@@ -14,3 +14,10 @@
     :members:
     :undoc-members:
     :show-inheritance:
+
+:mod:`niapy.callbacks`
+----------------------
+.. automodule:: niapy.callbacks
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/source/conf.py

@@ -19,7 +19,7 @@
 # -- Project information -----------------------------------------------------
 
 project = u'NiaPy'
-copyright = u'2018-2020, NiaOrg'
+copyright = u'2018-2023, NiaOrg'
 author = u'Grega Vrbančič, Lucija Brezočnik, Uroš Mlakar, Dušan Fister, Iztok Fister Jr., Klemen Berkovič, Jan Popič'
 
 # The short X.Y version
@@ -82,7 +82,7 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'press' #'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 html_logo = '_static/NiaPyLogo.png'
 
@@ -91,9 +91,8 @@
 # documentation.
 #
 html_theme_options = {
-    "external_links": [
-      ("Github", "https://github.com/NiaOrg/NiaPy"),
-    ]
+    "logo_only": True,
+    "display_version": False,
 }
 
 # Add any paths that contain custom static files (such as style sheets) here,
@@ -200,6 +199,3 @@
 napoleon_use_rtype = True
 napoleon_use_keyword = True
 napoleon_custom_sections = None
-
-import matplotlib
-matplotlib.use('agg')

docs/source/documentation.rst

@@ -6,11 +6,10 @@ Documentation
     We suppose that you already followed the :doc:`/installation` guide. If not, please do so
     before you continue to read this section.
 
-To locally generate and preview documentation run the following command in the project root folder:
+To locally generate the documentation run the following command in the project root folder:
 
 .. code-block:: bash
 
-    pipenv run sphinx-autobuild docs/source docs/build/html
-
-If the build of the documentation is successful, you can preview the documentation by navigating to the http://127.0.0.1:8000.
+    poetry run sphinx-build docs/source docs/build/html
 
+You can then view it by opening docs/build/html/index.html in your browser

docs/source/index.rst

@@ -3,11 +3,6 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-.. _reference:
-
-.. image:: _static/NiaPyLogo.png
-    :align: center
-
 NiaPy's documentation
 =================================
 
@@ -28,7 +23,7 @@ implementing algorithms from scratch.
 
 * **Free software:** MIT license
 * **Github repository:** https://github.com/NiaOrg/NiaPy
-* **Python versions:** 3.9.x, 3.10.x, 3.11.x
+* **Python versions:** 3.9.x, 3.10.x, 3.11.x, 3.12.x
 
 The main documentation is organized into a couple sections:
 
@@ -74,6 +69,7 @@ The main documentation is organized into a couple sections:
 .. _api-docs:
 
 .. toctree::
-  :caption: API Documentation
+   :maxdepth: 2
+   :caption: API Documentation
 
-  api/index
+   api/index

docs/source/installation.rst

@@ -14,26 +14,18 @@ Requirements
 Installation of development dependencies
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-**NiaPy dependencies:**
-
-+-----------+-----------+----------+
-| Package   | Version   | Platform |
-+===========+===========+==========+
-| numpy     | >=1.26.1  | All      |
-+-----------+-----------+----------+
-| matplotlib| >=3.8.0   | All      |
-+-----------+-----------+----------+
-| pandas    | >=2.1.1   | All      |
-+-----------+-----------+----------+
-| openpyxl  | >=3.1.2   | All      |
-+-----------+-----------+----------+
-
 Install project dependencies into a virtual environment:
 
 .. code-block:: bash
 
     poetry install
 
+Install documentation dependencies with:
+
+.. code-block:: bash
+
+    poetry install --with docs
+
 Run tests with:
 
 .. code-block:: bash

docs/source/testing.rst

@@ -16,7 +16,7 @@ For the purpose of checking if all test are passing locally you can run followin
 
 .. code-block:: bash
 
-    make test
+    poetry run pytest
 
 If all tests passed running this command it is most likely that the tests would pass on
 our build system to.