project_setup updated

project_setup.md

@@ -1,70 +1,44 @@
 # Project Setup
 
-Here we provide some details about the project setup. Most of the choices are explained in the
-[guide](https://guide.esciencecenter.nl). Links to the relevant sections are included below. Feel free to remove this
-text when the development of the software package takes off.
-
-For a quick reference on software development, we refer to [the software guide
-checklist](https://guide.esciencecenter.nl/#/best_practices/checklist).
-
 ## Python versions
 
 This repository is set up with Python versions:
 
-- 3.8
-- 3.9
-- 3.10
 - 3.11
 - 3.12
 
-Add or remove Python versions based on project requirements. See [the
-guide](https://guide.esciencecenter.nl/#/best_practices/language_guides/python) for more information about Python
-versions.
-
 ## Package management and dependencies
 
-You can use either pip or conda for installing dependencies and package management. This repository does not force you
-to use one or the other, as project requirements differ. For advice on what to use, please check [the relevant section
-of the
-guide](https://guide.esciencecenter.nl/#/best_practices/language_guides/python?id=dependencies-and-package-management).
+For installing the dependencies and package management, [micromamba](https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html) and [poetry](https://python-poetry.org/) have been used.
 
-- Runtime dependencies should be added to `pyproject.toml` in the `dependencies` list under `[project]`.
-- Development dependencies should be added to `pyproject.toml` in one of the lists under `[project.optional-dependencies]`.
+The dependencies are listed in the `pyproject.toml` file under the section `[tool.poetry.dependencies]` and `[tool.poetry.group.dev.dependencies]`.
 
 ## Packaging/One command install
 
-You can distribute your code using PyPI.
-[The guide](https://guide.esciencecenter.nl/#/best_practices/language_guides/python?id=building-and-packaging-code) can
-help you decide which tool to use for packaging.
+To create a new environment, use the micromamba:
+
+```console
+micromamba create rcx-tk
+micromamba activate rcx-tk
+```
+To install all dependencies specified in the `pyproject.toml` file, use poetry:
+
+```console
+poetry install
+```
 
 ## Testing and code coverage
 
-- Tests should be put in the `tests` folder.
-- The `tests` folder contains:
-  - Example tests that you should replace with your own meaningful tests (file: `test_my_module.py`)
+- Tests are in the `tests` folder, in the `test_process_metadata_file.py` file.
 - The testing framework used is [PyTest](https://pytest.org)
-  - [PyTest introduction](https://pythontest.com/pytest-book/)
-  - PyTest is listed as a development dependency
-  - This is configured in `pyproject.toml`
 - The project uses [GitHub action workflows](https://docs.github.com/en/actions) to automatically run tests on GitHub infrastructure against multiple Python versions
-  - Workflows can be found in [`.github/workflows`](.github/workflows/)
-- [Relevant section in the guide](https://guide.esciencecenter.nl/#/best_practices/language_guides/python?id=testing)
 
 ## Documentation
 
-- Documentation should be put in the [`docs/`](docs/) directory. The contents have been generated using `sphinx-quickstart` (Sphinx version 1.6.5).
-- We recommend writing the documentation using Restructured Text (reST) and Google style docstrings.
-  - [Restructured Text (reST) and Sphinx CheatSheet](https://thomas-cokelaer.info/tutorials/sphinx/rest_syntax.html)
-  - [Google style docstring examples](http://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
+- Documentation is in the [`docs/`](docs/) directory. The contents have been generated using `sphinx-quickstart` (Sphinx version 1.6.5).
 - The documentation is set up with the ReadTheDocs Sphinx theme.
-  - Check out its [configuration options](https://sphinx-rtd-theme.readthedocs.io/en/latest/).
 - [AutoAPI](https://sphinx-autoapi.readthedocs.io/) is used to generate documentation for the package Python objects.
 - `.readthedocs.yaml` is the ReadTheDocs configuration file. When ReadTheDocs is building the documentation this package and its development dependencies are installed so the API reference can be rendered.
-- [Relevant section in the guide](https://guide.esciencecenter.nl/#/best_practices/language_guides/python?id=writingdocumentation)
-
-## Coding style conventions and code quality
-
-- [Relevant section in the NLeSC guide](https://guide.esciencecenter.nl/#/best_practices/language_guides/python?id=coding-style-conventions) and [README.dev.md](README.dev.md).
 
 ## Continuous code quality
 
@@ -75,43 +49,8 @@ help you decide which tool to use for packaging.
 
 ## Package version number
 
-- We recommend using [semantic versioning](https://guide.esciencecenter.nl/#/best_practices/releases?id=semantic-versioning).
-- For convenience, the package version is stored in a single place: `rcx-tk/pyproject.toml` under the `tool.bumpversion` header.
-- Don't forget to update the version number before [making a release](https://guide.esciencecenter.nl/#/best_practices/releases)!
-
-## Logging
-
-- We recommend using the logging module for getting useful information from your module (instead of using print).
-- The project is set up with a logging example.
-- [Relevant section in the guide](https://guide.esciencecenter.nl/#/best_practices/language_guides/python?id=logging)
+- Releases are labelled using the [semantic versioning](https://guide.esciencecenter.nl/#/best_practices/releases?id=semantic-versioning).
 
 ## CHANGELOG.md
 
-- Document changes to your software package
-- [Relevant section in the guide](https://guide.esciencecenter.nl/#/best_practices/releases?id=changelogmd)
-
-## CITATION.cff
-
-- To allow others to cite your software, add a `CITATION.cff` file
-- It only makes sense to do this once there is something to cite (e.g., a software release with a DOI).
-- Follow the [making software citable](https://guide.esciencecenter.nl/#/citable_software/making_software_citable) section in the guide.
-
-## CODE_OF_CONDUCT.md
-
-- Information about how to behave professionally
-- [Relevant section in the guide](https://guide.esciencecenter.nl/#/best_practices/documentation?id=code-of-conduct)
-
-## CONTRIBUTING.md
-
-- Information about how to contribute to this software package
-- [Relevant section in the guide](https://guide.esciencecenter.nl/#/best_practices/documentation?id=contribution-guidelines)
-
-## MANIFEST.in
-
-- List non-Python files that should be included in a source distribution
-- [Relevant section in the guide](https://guide.esciencecenter.nl/#/best_practices/language_guides/python?id=building-and-packaging-code)
-
-## NOTICE
-
-- List of attributions of this project and Apache-license dependencies
-- [Relevant section in the guide](https://guide.esciencecenter.nl/#/best_practices/licensing?id=notice)
+- To document the changes, we use the [CHANGELOG.md](https://github.com/RECETOX/rcx-tk/blob/master/CHANGELOG.md)