Update code format in docs #24

docs/development/best-practice/code_style.md

@@ -49,3 +49,6 @@ Following good documentation practices ensures code is understandable to others.
 Maintain a logical structure within files, grouping related functions and
 classes. Consider the readability of your code and strive for modular,
 well-organized files.
+
+!!! note "Used Icons"
+    🐙 GitHub | 💠 git | 📝 File | 💻 Command Line

docs/development/best-practice/continuous_integration.md

@@ -45,8 +45,8 @@ for testing:
 ### Install
 
 Install the required package in a python environment. <br>
-💻 `pip install tox` install tox <br>
-💻 `tox` run tox locally
+   💻 `pip install tox` Install tox <br>
+   💻 `tox` Run tox locally
 
 
 ## Adding and Managing Tests

docs/development/best-practice/index.md

@@ -21,3 +21,6 @@ high standards in a collaborative scientific software environment:
 
 Following these practices will streamline development, reduce bugs, and foster a
 productive, collaborative coding environment.
+
+!!! note "Used Icons"
+    🐙 GitHub | 💠 git | 📝 File | 💻 Command Line

docs/development/best-practice/test_driven_development.md

@@ -57,11 +57,11 @@ of testing, such as edge cases and integration scenarios.
 This example demonstrates the TDD approach within a Django app. <br>
 You can run all tests in Django using the following command:
 
-💻 `python manage.py test`
+    💻 `python manage.py test`
 
 To run specific test cases, you can provide the app name and the test case:
 
-💻 `python manage.py test app.MyModelViewTestCase`
+    💻 `python manage.py test app.MyModelViewTestCase`
 
 This is a Step-by-Step Guide to TDD in Django:
 

docs/development/collaboration/chat.md

@@ -1,12 +1,15 @@
 # Chat
 
-For direct communication, this repo uses a public [Element](https://element.io/) room. <br>
+For direct communication, this repository uses a public [Element](https://element.io/) room. <br>
 This messenger platform is based on the [[matrix]](https://en.wikipedia.org/wiki/Matrix_(protocol))
 communication protocol <br>
 and can be accessed without a mobile phone.
 
 To engage with the developer and user community, <br>
-login with an existing account (e.g. GitHub) or register a new account.
+login with an existing account (for example GitHub) or register a new account.
 
 The room name is:
-[Super-Repo:matrix.org](https://app.element.io/#/room/#super-repo:matrix.org). <br>
+[Super-Repository:matrix.org](https://app.element.io/#/room/#super-repository:matrix.org). <br>
+
+!!! note "Used Icons"
+    🐙 GitHub | 💠 git | 📝 File | 💻 Command Line

docs/development/collaboration/code_of_conduct.md

@@ -1,7 +1,10 @@
 # Code of Conduct
 
-This repository is following the [Contributor Covenant Code of Conduct](https://github.com/rl-institut/super-repo/blob/production/CODE_OF_CONDUCT.md). <br>
+This repository is following the [Contributor Covenant Code of Conduct](https://github.com/rl-institut/super-repository/blob/production/CODE_OF_CONDUCT.md). <br>
 
 Everyone is asked to be self-reflective and always maintain a good culture
 of discussion and active participation.
-This includes written communication in this repo and direct encounters in meetings and events.
+This includes written communication in this repository and direct encounters in meetings and events.
+
+!!! note "Used Icons"
+    🐙 GitHub | 💠 git | 📝 File | 💻 Command Line

docs/development/collaboration/git.md

@@ -44,7 +44,7 @@ It includes all needed information to merge branches and release new versions.
 
 GitHub Labels are used to organize Issues and PR. <br>
 Colours and emoticons improve presentation, see: <br>
-📝 [github-labels.json](https://github.com/rl-institut/super-repository/blob/develop/docs/development/git/github-labels.json)
+    📝 [github-labels.json](https://github.com/rl-institut/super-repository/blob/develop/docs/development/git/github-labels.json)
 
 ## GitHub Workflows (Actions)
 
@@ -62,8 +62,8 @@ It is used to improve auto-format code, do linting and run tests before every co
 ### Install
 
 Install the required package in a python environment. <br>
-💻 `pip install pre-commit` install pre-commit <br>
-💻 `pre-commit install` install pre-commit
+    💻 `pip install pre-commit` Install pre-commit <br>
+    💻 `pre-commit install` Install pre-commit
 
 ### Setup
 
@@ -81,17 +81,17 @@ List of implemented hooks:
 
 ### Use
 
-All commits will trigger the hooks automatically.<br>
-💠 `git commit file -m "Commit message #IssueNr"` to commit
+All commits will trigger the hooks automatically. <br>
+    💠 `git commit file -m "Commit message #IssueNr"` Commit with message
 
-Commit without running the hooks.<br>
-💠 `git commit --no-verify file` to commit without hooks
+Commit without running the hooks. <br>
+    💠 `git commit --no-verify file` Commit without hooks
 
 !!! note "Line endings"
     There can be problems with file line endings on Windows, `CRLF` is used on Windows and `LF` is used on Linux.
 
-To run the hooks on all files in your repository use:<br>
-💻 `pre-commit run --all-files`
+To run the hooks on all files in your repository use: <br>
+    💻 `pre-commit run --all-files` Run pre-commit hooks
 
 !!! warning "Markdown files / Admonitions"
     If the hook is applied to markdown files that include special formatting,

docs/development/collaboration/index.md

@@ -5,8 +5,11 @@ The repository has several elements to provide necessary functions.
 
 To participate in the development you can do the following:
 
-- Contribute to the [GitHub Discussions](https://github.com/rl-institut/super-repo/discussions)
-- Contribute to the [GitHub Issues](https://github.com/rl-institut/super-repo/issues)
-- Follow the [workflow for collaborative development](https://github.com/rl-institut/super-repo/blob/production/CONTRIBUTING.md)
-- Get in touch with the community on the [Element Chat](https://rl-institut.github.io/super-repo/develop/development/collaboration/chat/)
-- Meet the developers in one of the [regular meetings](https://rl-institut.github.io/super-repo/develop/development/collaboration/meeting/)
+- Contribute to the [GitHub Discussions](https://github.com/rl-institut/super-repository/discussions)
+- Contribute to the [GitHub Issues](https://github.com/rl-institut/super-repository/issues)
+- Follow the [workflow for collaborative development](https://github.com/rl-institut/super-repository/blob/production/CONTRIBUTING.md)
+- Get in touch with the community on the [Element Chat](https://rl-institut.github.io/super-repository/develop/development/collaboration/chat/)
+- Meet the developers in one of the [regular meetings](https://rl-institut.github.io/super-repository/develop/development/collaboration/meeting/)
+
+!!! note "Used Icons"
+    🐙 GitHub | 💠 git | 📝 File | 💻 Command Line

docs/development/collaboration/license_and_citation.md

@@ -5,7 +5,7 @@
 This software is developed under an
 [open-source license](https://en.wikipedia.org/wiki/Open-source_license). <br>
 The selected license can be read in the
-[LICENSE.txt](https://github.com/rl-institut/super-repo/blob/production/LICENSE.txt).
+[LICENSE.txt](https://github.com/rl-institut/super-repository/blob/production/LICENSE.txt).
 
 The users have permission to
 [run and use, modify, distribute the program, and release the improvements](https://www.gnu.de/free-software/index.de.html)
@@ -14,7 +14,7 @@ include the license text.
 
 Please attribute as:
 
-**"Super-Repo" © Reiner Lemoine Institut | MIT License**
+**"Super-Repository" © Reiner Lemoine Institut | MIT License**
 
 ### REUSE
 
@@ -23,8 +23,8 @@ specification.
 All files are explicitly stating the corresponding license and copyright information.
 It is implemented as GitHub workflow and pre-commit hook:
 
-- GitHub workflow: [reuse.yml](https://github.com/rl-institut/super-repo/blob/feature-7-REUSE/.github/workflows/reuse.yml)
-- [Pre-commit hook](https://github.com/rl-institut/super-repo/blob/feature-7-REUSE/.pre-commit-config.yaml#L66)
+- GitHub workflow: [reuse.yml](https://github.com/rl-institut/super-repository/blob/feature-7-REUSE/.github/workflows/reuse.yml)
+- [Pre-commit hook](https://github.com/rl-institut/super-repository/blob/feature-7-REUSE/.pre-commit-config.yaml#L66)
 
 All copyright information should follow this example:
 
@@ -39,11 +39,14 @@ SPDX-License-Identifier: {$SPDX_license_name}
 
 To [scientifically cite](https://en.wikipedia.org/wiki/Quotation) this
 repository, see the **_Cite this repository_** function or the file
-[CITATION.cff](https://github.com/rl-institut/super-repo/blob/production/CITATION.cff).
+[CITATION.cff](https://github.com/rl-institut/super-repository/blob/production/CITATION.cff).
 
 ## Contributing
 
 Since this software is under an open source license and can be downloaded,
 run and modified, you are invited to comment, improve and develop the program as you wish. <br>
 To contribute to the **collaborative development** follow the workflow described in
-[CONTRIBUTING.md](https://github.com/rl-institut/super-repo/blob/production/CONTRIBUTING.md).
+[CONTRIBUTING.md](https://github.com/rl-institut/super-repository/blob/production/CONTRIBUTING.md).
+
+!!! note "Used Icons"
+    🐙 GitHub | 💠 git | 📝 File | 💻 Command Line

docs/development/collaboration/meeting.md

@@ -4,7 +4,7 @@ In order to develop a program collaboratively, it is helpful to regularly
 exchange information about the current status and to discuss open questions
 and make decisions. <br>
 If you want to join the meetings, please use the
-[GitHub Discussions](https://github.com/rl-institut/super-repo/discussions).
+[GitHub Discussions](https://github.com/rl-institut/super-repository/discussions).
 
 ## Developer Meetings
 
@@ -14,7 +14,7 @@ the general vision of software development.
 
 The regular developer meeting takes place on <br>
 **the first Wednesday of the month between 9 and 9:30 am**. <br>
-The meeting room is: [meet.jit.si/super-repo-dev](https://meet.jit.si/super-repo-dev)
+The meeting room is: [meet.jit.si/super-repository-dev](https://meet.jit.si/super-repository-dev)
 
 ## User Meetings
 
@@ -25,3 +25,6 @@ or give general feedback.
 The regular user meeting takes place after the developer meeting in the same
 room on the <br>
 **first Wednesday of the month between 9:30 and 10 am**.
+
+!!! note "Used Icons"
+    🐙 GitHub | 💠 git | 📝 File | 💻 Command Line

docs/development/collaboration/users.md

@@ -3,9 +3,7 @@
 Known user of this software can be added to
 📝 [USERS.cff](https://github.com/rl-institut/super-repository/blob/production/USERS.cff)
 for reference. <br>
-Please use the 📝 `issue_template_user_kudos.md`.
-
-
+Please use the issue template: 📝 `issue_template_user_kudos.md`
 
 !!! note "Used Icons"
     🐙 GitHub | 💠 git | 📝 File | 💻 Command Line

docs/development/documentation/index.md

@@ -20,21 +20,21 @@ additional features and an elegant design. <br>
 ### Install
 
 Install the required packages in a python environment. <br>
-💻 `pip install mkdocs` install MkDocs <br>
-💻 `pip install mkdocs-material` install the material theme
+    💻 `pip install mkdocs` Install MkDocs <br>
+    💻 `pip install mkdocs-material` Install the material theme
 
 ### Build
 
 Generate the documentation locally. <br>
-💻 `mkdocs serve` start the local live version of the documentation <br>
-💻 `mkdocs build` create a folder `site` with the documentation
+    💻 `mkdocs serve` Start the local live version of the documentation <br>
+    💻 `mkdocs build` Create a folder `site` with the documentation
 
 ### Publish
 
 #### Manually
 
 Publish documentation on **GitHub Pages**. <br>
-💻 `mkdocs gh-deploy` manually deploys the documentation files
+    💻 `mkdocs gh-deploy` Manually deploys the documentation files
 
 !!! warning "Manually deploy documentation"
     This command overrides all manually deployed versions (mike). <br>
@@ -49,34 +49,34 @@ A commit on the `develop` branch starts the workflow.
 #### Mike
 
 The package [mike](https://github.com/jimporter/mike) is used to deploy [multiple versions](https://squidfunk.github.io/mkdocs-material/setup/setting-up-versioning/?h=versioning) of the documentation.<br>
-💻 `pip install mike` install mike <br>
-💻 `mike deploy --push --update-aliases 0.1 latest` deploys the latest version <br>
-💻 `mike set-default --push latest` Set the default version to latest <br>
-💻 `mike deploy develop --push` deploys the develop branch
+    💻 `pip install mike` Install mike <br>
+    💻 `mike deploy --push --update-aliases 0.1 latest` Deploys the latest version <br>
+    💻 `mike set-default --push latest` Set the default version to latest <br>
+    💻 `mike deploy develop --push` Deploys the develop branch
 
 !!! note "Mike Versions"
     It is recommended to use only the **Minor Versions** (for example 0.1) and exclude the **Patch Version** (for example 0.1.1)!
 
 Other useful commands are: <br>
-💻 `mike serve` test mike on [`http://localhost:8000`](http://localhost:8000) <br>
-💻 `mike list` list all versions <br>
-💻 `mike retitle 1.0.0 1.0.1 --push` rename a version <br>
-💻 `mike delete 0.1 --push` deletes a specific versions <br>
-💻 `mike delete --all --push` deletes all versions
+    💻 `mike serve` Test mike on [`http://localhost:8000`](http://localhost:8000) <br>
+    💻 `mike list` List all versions <br>
+    💻 `mike retitle 1.0.0 1.0.1 --push` Rename a version <br>
+    💻 `mike delete 0.1 --push` Deletes a specific versions <br>
+    💻 `mike delete --all --push` Deletes all versions
 
 When adding older versions, load the `Git Tags` used for the releases: <br>
-💠 `git checkout v0.1.1` <br>
-💻 `mike deploy 0.1 --push` deploys the old version 0.1
+    💠 `git checkout v0.1.1` <br>
+    💻 `mike deploy 0.1 --push` Deploys the old version 0.1
 
 When building mike locally, the branch `gh-pages` is modified locally. <br>
-💻 `error: gh-pages is unrelated to origin/gh-pages` <br>
-💠 `git branch -D gh-pages` delete the local documentation branch
+    💻 `error: gh-pages is unrelated to origin/gh-pages` <br>
+    💠 `git branch -D gh-pages` Delete the local documentation branch
 
 ## mkdocstrings
 
 [mkdocstrings](https://mkdocstrings.github.io/) generates automatic
 documentation (autodocs) from [Google style docstrings](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html). <br>
-💻 `pip install mkdocstrings` install mkdocstrings
+    💻 `pip install mkdocstrings` Install mkdocstrings
 
 !!! note "Used Icons"
     🐙 GitHub | 💠 git | 📝 File | 💻 Command Line

docs/development/release/index.md

@@ -7,26 +7,27 @@ The software release has four main goals:
 3. Update the documentation
 4. Publish a new version of the package at PyPI
 
-The [RELEASE_PROCEDURE.md](https://github.com/rl-institut/super-repository/blob/production/RELEASE_PROCEDURE.md)
+The 📝 [RELEASE_PROCEDURE.md](https://github.com/rl-institut/super-repository/blob/production/RELEASE_PROCEDURE.md)
 contain detailed instructions to do a release.
 
 ## Automated Versioning with Bumpversion
 
 **Bumpversion** is a tool for automated version management in software projects. <br>
-It ensures consistent version updates across files and documentation. <br>
-By specifying a part to increment (major, minor, or patch), Bumpversion updates
-the version number and creates a Git commit or tag automatically.
-This streamlines release workflows, reduces human error, and keeps project versioning synchronized.  
+It ensures consistent version updates across files and documentation <br>
+by specifying a part to increment (major, minor, or patch). <br>
+This streamlines release workflows and keeps project versioning synchronized.
 
 Install package:  
-💻 `pip install --upgrade bump-my-version`
-
-For configuration, create a `.bumpversion.toml` file to specify versioning rules and affected files.
+    💻 `pip install --upgrade bump-my-version` <br>
+    📝 `.bumpversion.toml` Configuration file for versioning rules and affected files
 
 Test bumpversion: <br>
-💻 `bump-my-version show-bump` Preview next possible versions <br>
-💻 `bump-my-version bump minor --dry-run -vv` Sandbox bump
+    💻 `bump-my-version show-bump` Preview next possible versions <br>
+    💻 `bump-my-version bump minor --dry-run -vv` Sandbox bump
 
 Use bumpversion: <br>
-💻 `bump-my-version --current-version 0.2.0 mino`
-💠 `git commit file -am "Bumpversion #IssueNr"` to commit bump
+    💻 `bump-my-version --current-version 0.2.0 mino` <br> Run bumpversion
+    💠 `git commit file -am "Bumpversion #IssueNr"` Commit bumpversion changes
+
+!!! note "Used Icons"
+    🐙 GitHub | 💠 git | 📝 File | 💻 Command Line

docs/index.md

@@ -4,9 +4,9 @@ hide:
   - toc
 ---
 
-# Welcome to the Super-Repo Documentation
+# Welcome to the Super-Repository Documentation
 
-A template repo to test and document elements and features for research software. <br>
+A template repository to test and document elements and features for research software. <br>
 It implements the collection of repository elements and files. <br>
 The goal is to simplify and standardise the creation of software in GitHub repositories.
 
@@ -20,17 +20,15 @@ The documentation is separated into two main sections:
 Files and structures related to collaborative development, community processes,
 and documentation.
 
-- COLLABORATION
-- GIT
-- CODE-STYLE
-- DOCUMENTATION
-- RELEASE
+- [Collaboration](https://rl-institut.github.io/super-repository/develop/development/collaboration/)
+- [Best-Practices](https://rl-institut.github.io/super-repository/develop/development/best-practice/)
+- [Documentation](https://rl-institut.github.io/super-repository/develop/development/documentation/)
+- [Release](https://rl-institut.github.io/super-repository/develop/development/release/)
 
 ### Fields for code documentation
 
 Methods and functions of the module.
 
-- INSTALL
-- FUNCTIONS
-- TESTS
-- LOGGING
+- [Install](https://rl-institut.github.io/super-repository/develop/user_documentation/install/)
+- [Functions](https://rl-institut.github.io/super-repository/develop/user_documentation/)
+- [Code Example](https://rl-institut.github.io/super-repository/develop/user_documentation/code_example/)