Field standard for Bioinformatics within Medical Laboratories
Which procedures need to be documented for the development of pipelines, workflows or tools.
- Python 3.10
Poetry is a tool for dependency management and packaging in Python. It allows you to declare the libraries your project depends on and it will manage (install/update) them for you. Poetry offers a lockfile to ensure repeatable installs.
Install Poetry via:
curl -sSL https://install.python-poetry.org | python3 -For more information go to.
To install the defined dependencies for your project, navigate to the project folder and execute:
poetry installYou want to contribute the VKGL Bioinformatics field standard, great! Strictly speaking the scheme below is not enforced, however strongly recommended to keep your changes grouped together in your git history. Commit your changes, do not hesitate to do that often, however make understandable commit messages. What is enforced in the end is a code review process to keep information accurate.
Using the git flow scheme is strongly encouraged to keep the history of the project orderly and concise. From a practical point of view using the git flow plugin is the easiest way (but not strictly necessary).
- Install the plugin.
- Init the plugin:
git flow init
# production: main
# development: develop
# feature: feature/
# bugfix: not used (keep default)
# release: release/
# hotfix: not used (keep default)
# support: not used (keep default)
# version tag prefix: []Additions to our field standard should be handed in via a feature branch. The feature branch should have a clear name that shortly describes your addition. Feature branches are located under feature/ in our repository. After initialization of the plugin starting a feature branch to write your addition to the field standard is easy:
git flow feature start "GREAT ADDITION"Pages are written using the markup language markdown. Some handies (feel free to add if you like more):
| Syntax | Description | Example |
|---|---|---|
| # H1 | Header line | table |
| - bullet | Bullet points | table |
| **bold** | Bold | bold |
| *italic | Italic | italic |
| `command` | Code | command |
| ```bash commands ``` | Code block (can use syntax highlighting by indicating the language) | this is a code block |
| [text](link) | Hyperlink | extended syntax |
|  | Image |  |
To start the development version first navigate to the project folder. Next run the command:
poetry run mkdocs serveThis starts a local development version that can be viewed in a browser via localhost:8000 or 127.0.0.1:8000.
You can push your feature to the main repository if you have access or to your own fork. After you are finished and everything looks decent enough you can hand in your addition by creating a pull request in github. After a code review by one of the team members your additions will be merged to our develop branch.
Once in a while, the team will revise the current document, and might release a new version of this norm. A revision of the norm document will include a release review by the team, during which the develop will be merged with the main branch. An update on the main branch will trigger a new version on the website.
The release procedure will start branching the main branch and merge the develop into this. This is done using the git flow plugin, using the following procedure:
git flow release start "VERSION NORM RELEASE CANDIDATE"A pull request for this release candidate onto the main branch will be created by the team, after which a last round of feedback is initiated.
If the team agrees the release candidate is ready for publication the pull request is merged, after which it will be publicated on the website.