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Merge pull request #569 from NLeSC/423_user_documentation
423-update user documentation
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CHANGELOG.md

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* Make online documentation optional [#476](https://github.com/NLeSC/python-template/pull/476)
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### Changed
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* Updated the user documentation (README.md) of the template [#569](https://github.com/NLeSC/python-template/pull/569)
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* Droped Python 3.8 and 3.9 support [#551](https://github.com/NLeSC/python-template/pull/551)
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* Fix broken link checker [#546](https://github.com/NLeSC/python-template/pull/546)
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* pre-commit script is optional ([#457](https://github.com/NLeSC/python-template/issues/457))

README.md

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# Netherlands eScience Center Python Template
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Spend less time setting up and configuring your new Python packages and comply with the [Netherlands eScience Center Software Development Guide](https://guide.esciencecenter.nl/) from the start.
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Spend less time setting up and configuring your new Python packages which includes research software good practices from the start.
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Use this [Copier](https://copier.readthedocs.io) template to generate an empty Python package. Features include:
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### Scenario 1: Create a new package
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#### Step 1/2: Create the files and directory structure
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Run `copier copy` with the template:
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```shell
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# Notes:
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# 1. Make sure that `path/to/destination` is an empty directory
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# 2. See table below for explanation of each question
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# 3. The files will be generated in the specified destination directory
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copier copy https://github.com/nlesc/python-template.git path/to/destination
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```
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| Name | Default value | Explanation |
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| ------------------------- | ------------- | ----------- |
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| package_name | my_python_package | Name of the package. Avoid using spaces, dashes, or uppercase letters for the best experience across operating systems. This also will be used as the github repository name.|
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| package_short_description | Short description of package | The information that you enter here will end up in the README, documentation, license, and pyproject.toml, so it may be a good idea to prepare something in advance. |
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| keyword1 | keyword1 | A term that describes your package. |
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| keyword2 | keyword2 | Another term that describes your package. |
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| version | 0.1.0 |   |
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| github_organization | <my-github-organization> | GitHub organization that will contain this project's repository. This can also be your GitHub user name. |
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| license | Apache Software License 2.0 | The software license under which the code is made available. |
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| full_name | Jane Smith | Your full name, e.g. _Jane Smith_. |
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| email | yourname@esciencecenter.nl | Your (work) email address. |
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| copyright_holder | Netherlands eScience Center | Name(s) of the organization(s) or person(s) who hold the copyright of the software. |
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| code_of_conduct_email | yourname@esciencecenter.nl | Email address of the person who should be contacted in case of violations of the Code of Conduct. |
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Once the project files have been generated, follow the steps outlined in
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[next_steps.md](template/next_steps.md.jinja).
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#### Step 2/2: Read about what was just generated
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Good job! You have now generated the skeleton for your package:
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```text
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.
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├── CHANGELOG.md
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├── CITATION.cff
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├── CODE_OF_CONDUCT.md
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├── CONTRIBUTING.md
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├── .copier-answers.yml
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├── docs
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│   ├── conf.py
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│   ├── index.rst
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│   ├── make.bat
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│   ├── Makefile
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│   └── _templates
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│   └── .gitignore
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├── .editorconfig
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├── .githooks
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│   └── pre-commit
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├── .github
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│   ├── next_steps
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│   │   ├── 01_sonarcloud_integration.md
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│   │   ├── 02_citation.md
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│   │   ├── 03_readthedocs.md
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│   │   ├── 04_zenodo_integration.md
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│   │   └── 05_linting.md
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│   └── workflows
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│   ├── build.yml
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│   ├── cffconvert.yml
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│   ├── documentation.yml
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│   ├── markdown-link-check.yml
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│   ├── next_steps.yml
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│   └── sonarcloud.yml
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├── .gitignore
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├── MANIFEST.in
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├── .mlc-config.json
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├── next_steps.md
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├── NOTICE
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├── project_setup.md
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├── pyproject.toml
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├── README.dev.md
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├── README.md
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├── .readthedocs.yaml
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├── sonar-project.properties
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├── src
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│   └── my_python_package
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│   ├── __init__.py
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│   └── my_module.py
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├── tests
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│   ├── __init__.py
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│   ├── test_my_module.py
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│   ├── test_project.py
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│   └── test_values.py
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└── .zenodo.json
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```
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> [!NOTE]
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> 1. Make sure that `path/to/destination` is an empty directory
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> 1. Based on the profile and selected features, the package will be generated in the specified destination directory
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For an explanation of what's there, read on in the [project_setup.md](template/project_setup.md.jinja) file.
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For an explanation of what's there, read on in the `project_setup.md` file.
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### Scenario 2: Apply to pre-existing code
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