Add Readthedocs Documentation for DisCoTec (#133)

* docs: add basic doxygen and sphinx configuration and readthedocs config
* docs: add Doxygen markup to most important classes
* docs: add some docs in .rst format, some adapted from READMEs
* docs: rework some READMEs
* remove some unused functions and includes
* adds Code of Conduct and Contributing guideline
* tests: have slightly longer timeouts

---------

Co-authored-by: Theresa Pollinger <[email protected]>
Co-authored-by: Michael Obersteiner <[email protected]>
Co-authored-by: Alexander Van Craen <[email protected]>

.gitignore

@@ -36,7 +36,6 @@ pysgpp/pysgpp_wrap.h
 #ignoreing build output
 lib/sgpp/*
 *.log
-Doxyfile
 base/doc/doxygen/examples.doxy
 base/doc/doxygen/modules.doxy
 
@@ -97,3 +96,9 @@ coverage
 
 # ignoring heaptrack output files
 heaptrack.*
+
+# ignoring documentation generated files
+docs/_*
+docs/api/
+docs/generated_docs/
+generated_docs/

.readthedocs.yaml

@@ -0,0 +1,26 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# 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:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+  jobs:
+    pre_build:
+      - doxygen docs/Doxyfile
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+  - requirements: docs/requirements.txt

CODE_OF_CONDUCT.md

@@ -0,0 +1,128 @@
+# 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, 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
+[[email protected]](mailto:[email protected]).
+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 2.0, available at
+<https://www.contributor-covenant.org/version/2/0/code_of_conduct.html>.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+<https://www.contributor-covenant.org/faq>. Translations are available at
+<https://www.contributor-covenant.org/translations>.

CONTRIBUTING.md

@@ -0,0 +1,47 @@
+# Contributing
+
+## Report a Bug
+
+If you encounter a bug, please write an [issue](https://github.com/SGpp/DisCoTec/issues),
+describing the system and environment where you encountered the error.
+If you are using Spack, please include the output of `spack spec discotec`
+(to your installed discotec version) and/or `spack load --list` if you are
+using spack modules.
+
+### Share Compilation Pain
+
+If you find yourself in the very common (but sometimes seemingly endless)
+pain of compilation on HPC systems, feel free to open an issue as well.
+If it is a problem in the DisCoTec Spack package or CMake setup, our
+contributors may be able to solve it, otherwise they may be able to give
+pointers to common solutions.
+
+### Get DisCoTec Help
+
+If you run into any combination technique or DisCoTec programming trouble,
+please also raise an issue. We know that the [documentation](https://discotec.readthedocs.io/)
+may be insufficient in places, but we need your feedback to know
+where to expand!
+
+## Solve an Issue or Contribute a Feature
+
+To find a good place to start coding, have a look at the
+[issue tracker](https://github.com/SGpp/DisCoTec/issues) and comment if
+you start working on an issue.
+
+If you want to implement a new feature not mentioned in the issues,
+please also create an issue to prevent duplicate work.
+
+DisCoTec uses the Google bracket style (2 spaces) and camelCase naming
+convention; member variables are appended with `_`.
+
+If you are not affiliated with the SGpp Team, we typically expect you
+develop the code on your fork and create a pull request for review.
+Please include (unit) tests in the [./tests](/tests) folder.
+Reviews will be based on function, understandability, and testability /
+test coverage.
+
+## Something else? Get in touch
+
+If you want to contribute in another way or collaborate with The SGpp Team,
+get in touch at <[email protected]>.