added initial structure rtd

aimclub · DenisSidoren · Jul 1, 2022 · Jun 7, 2022 · Jun 15, 2022 · Jun 15, 2022
commit 5f8ae8b956e91bab777dc9c0dec778ac5e663e44
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -0,0 +1,16 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+
+
+python:
+  version: 3.7
+  install:
+    - requirements: requirements.txt
diff --git a/docs/Makefile b/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     = source
+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)
diff --git a/docs/gefest/gefest.rst b/docs/gefest/gefest.rst
@@ -0,0 +1,4 @@
+Intro to GEFEST
+==============
+
+some information
diff --git a/docs/gefest/index.rst b/docs/gefest/index.rst
@@ -0,0 +1,12 @@
+GEFEST
+=====
+
+**That is all about GEFEST**
+
+.. toctree::
+   :glob:
+   :maxdepth: 1
+
+   gefest
+   installation
+   quickstart
diff --git a/docs/gefest/installation.rst b/docs/gefest/installation.rst
@@ -0,0 +1,18 @@
+Installation from GitHub
+========================
+  | git clone https://github.com/ITMO-NSS-team/GEFEST.git
+  | cd GEFEST
+  | pip install .
+  | pytest -s test/
+
+or full installation
+
+  | git clone https://github.com/ITMO-NSS-team/GEFEST.git
+  | cd FEDOT
+  | pip install .[extra]
+  | pytest -s test/
+
+Installation from PyPI
+======================
+  | pip install gefest  # common
+  | pip install gefest[extra]  # full
diff --git a/docs/gefest/quickstart.rst b/docs/gefest/quickstart.rst
@@ -0,0 +1,10 @@
+Quickstart
+==========
+
+GEFEST Framework quick start guide
+
+How to install
+--------------
+.. code::
+
+ pip install gefest
diff --git a/docs/make.bat b/docs/make.bat
@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd
diff --git a/docs/source/about.rst b/docs/source/about.rst
@@ -0,0 +1,6 @@
+About us
+========
+
+The FEDOT is developed and maintained by the `NSS Lab <https://itmo-nss-team.github.io/>`__ team.
+
+Our laboratory is part of the National Center for Cognitive Technologies (ITMO University, Russia), which provides cutting-edge software and algorithmic solutions. We focus on natural systems simulations, generative design of real and virtual objects, data-driven modeling, automated machine learning.
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -0,0 +1,63 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath('../..'))
+
+# -- Project information -----------------------------------------------------
+
+project = 'GEFEST'
+copyright = '2021-2022, NSS Lab'
+author = 'NSS Lab'
+
+# The full version, including alpha/beta/rc tags
+release = '0.0.1'
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    "sphinx_rtd_theme",
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.autodoc.typehints',
+]
+autodoc_typehints = 'description'
+
+autodoc_mock_imports = ['objgraph', 'memory_profiler', 'gprof2dot', 'snakeviz']
+
+autodoc_member_order = 'bysource'
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+# html_theme = 'alabaster'
+html_theme = "sphinx_rtd_theme"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+# html_static_path = ['_static']
+master_doc = 'index'
diff --git a/docs/source/contribution.rst b/docs/source/contribution.rst
@@ -0,0 +1,179 @@
+Contribution
+============
+
+We welcome you to `check the existing
+issues <https://github.com/ITMO-NSS-team/GEFEST/issues>`__ for bugs or
+enhancements to work on. If you have an idea for an extension to GEFEST,
+please `file a new
+issue <https://github.com/ITMO-NSS-team/GEFEST/issues/new`__ so we can
+discuss it.
+
+Make sure to familiarize yourself with the project layout before making
+any major contributions.
+
+Instructions
+-----------------
+
+There is a presentation to help you to take your first steps to become a FEDOT contributor below.
+
+:download:`Want to implement a custom operation in GEFEST <path to guide file>`
+
+
+How to contribute
+-----------------
+
+The preferred way to contribute to GEFEST is to fork the `main
+repository <https://github.com/ITMO-NSS-team/GEFEST/>`__ on GitHub:
+
+1. Fork the `project repository <https://github.com/ITMO-NSS-team/GEFEST>`__:
+   click on the 'Fork' button near the top of the page. This creates a
+   copy of the code under your account on the GitHub server.
+
+2. Clone this copy to your local disk:
+
+   ::
+
+         $ git clone git@github.com:YourUsername/GEFEST.git
+         $ cd GEFEST
+
+3. Create a branch to hold your changes:
+
+   ::
+
+         $ git checkout -b my-contribution
+
+4. Make sure your local environment is setup correctly for development.
+   Installation instructions are almost identical to `the user
+   instructions <instructions file>`__ except that GEFEST should *not* be
+   installed. If you have GEFEST installed on your computer then make
+   sure you are using a virtual environment that does not have GEFEST
+   installed.
+
+5. Start making changes on your newly created branch, remembering to
+   never work on the ``main`` branch! Work on this copy on your
+   computer using Git to do the version control.
+
+6. To check your changes haven't broken any existing tests and to check
+   new tests you've added pass run the following (note, you must have
+   the ``nose`` package installed within your dev environment for this
+   to work):
+
+   ::
+
+         $ pytest -s
+
+7. When you're done editing and local testing, run:
+
+   ::
+
+         $ git add modified_files
+         $ git commit
+
+to record your changes in Git, then push them to GitHub with:
+
+::
+
+          $ git push -u origin my-contribution
+
+Finally, go to the web page of your fork of the FEDOT repo, and click
+'Pull Request' (PR) to send your changes to the maintainers for review.
+
+(If it looks confusing to you, then look up the `Git
+documentation <http://git-scm.com/documentation>`__ on the web.)
+
+Before submitting your pull request
+-----------------------------------
+
+Before you submit a pull request for your contribution, please work
+through this checklist to make sure that you have done everything
+necessary so we can efficiently review and accept your changes.
+
+If your contribution changes GEFEST in any way:
+
+-  Update the
+   `documentation <https://github.com/ITMO-NSS-team/GEFEST/tree/main/docs>`__
+   so all of your changes are reflected there.
+
+-  Update the
+   `README <https://github.com/ITMO-NSS-team/GEFEST/blob/main/README.md>`__
+   if anything there has changed.
+
+If your contribution involves any code changes:
+
+-  Update the `project unit
+   tests <https://github.com/ITMO-NSS-team/GEFEST/tree/main/test>`__ to
+   test your code changes.
+
+-  Make sure that your code is properly commented with
+   `docstrings <https://www.python.org/dev/peps/pep-0257/>`__ and
+   comments explaining your rationale behind non-obvious coding
+   practices.
+
+If your contribution requires a new library dependency:
+
+-  Double-check that the new dependency is easy to install via ``pip``
+   or Anaconda and supports Python 3. If the dependency requires a
+   complicated installation, then we most likely won't merge your
+   changes because we want to keep GEFEST easy to install.
+
+-  Add the required version of the library to
+   `requirements.txt <https://github.com/ITMO-NSS-team/GEFEST/blob/main/requirements.txt>`__
+
+Contribute to the documentation
+-------------------------------
+Take care of the documentation.
+
+All the documentation is created with the Sphinx autodoc feature. Use ..
+automodule:: <module_name> section which describes all the code in the module.
+
+-  If a new package with several scripts:
+
+   1. Go to `docs/source/gefest <https://github.com/ITMO-NSS-team/GEFEST/tree/main/docs/source/gefest>`__ and create new your_name_for_file.rst file.
+
+   2. Add a Header underlined with “=” sign. It’s crucial.
+
+   3. Add automodule description for each of your scripts. ::
+
+       .. automodule:: gefest.core.your.first.script.path
+          :members:
+          :undoc-members:
+          :show-inheritance:
+
+       .. automodule:: gefest.core.your.second.script.path
+          :members:
+          :undoc-members:
+          :show-inheritance:
+       ...
+
+   4. Add your_name_for_file to the toctree at docs/source/gefest/index.rst
+
+-  If a new module to the existed package:
+
+    Most of the sections are already described in `docs/source/gefest <https://github.com/ITMO-NSS-team/GEFEST/tree/main/docs/source/gefest>`__ , so you can:
+
+   -  choose the most appropriate and repeat 3-d step from the previous section.
+   -  or create a new one and repeat 2-3 steps from the previous section.
+
+-  If a new function or a class to the existing module:
+
+    Be happy. Everything is already done for you.
+
+After submitting your pull request
+----------------------------------
+
+After submitting your pull request,
+`Travis-CI <https://travis-ci.com/>`__ will automatically run unit tests
+on your changes and make sure that your updated code builds and runs on
+Python 3. We also use services that automatically check code quality and
+test coverage.
+
+Check back shortly after submitting your pull request to make sure that
+your code passes these checks. If any of the checks come back with a red
+X, then do your best to address the errors.
+
+Acknowledgements
+----------------
+
+This document guide is based at well-written `TPOT Framework
+contribution
+guide <https://github.com/EpistasisLab/tpot/blob/master/docs_sources/contributing.md>`__.
diff --git a/docs/source/faq.rst b/docs/source/faq.rst
@@ -0,0 +1,9 @@
+FAQ
+===
+
+Frequently asked questions and answers
+
+What is GEFEST?
+--------------
+
+Some information