mirror of https://github.com/msberends/AMR.git
85 lines
3.7 KiB
Markdown
85 lines
3.7 KiB
Markdown
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# Developer Guideline
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Welcome to the Developer Guideline of the `AMR` R package. This guideline explains about repository workflows and updates of package elements.
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## Copyright
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This R package and of its components are licensed under the [GNU General Public License (GPL) v2.0](https://github.com/msberends/AMR/blob/main/LICENSE). In a nutshell, this means that this package:
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- May be used for commercial purposes
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- May be used for private purposes
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- May **not** be used for patent purposes
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- May be modified, although:
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- Modifications **must** be released under the same license when distributing the package
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- Changes made to the code **must** be documented
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- May be distributed, although:
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- Source code **must** be made available when the package is distributed
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- A copy of the license and copyright notice **must** be included with the package.
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- Comes with a LIMITATION of liability
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- Comes with NO warranty
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## General Intended Git(Hub) Workflow
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All updates to the reposo should be done using `git commit`, preferably with the following predefined pre-commit Git hook.
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This repository provides automated semantic versioning and R documentation updates by using a pre-commit Git hook. When using `git commit`, a script will be run to increase the version number, update the date and R documentation. To set this up, run this command when working locally in the repository:
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```bash
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git config --local core.hooksPath ".github/prehooks"
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```
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Now, when using `git commit`:
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```bash
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git commit -am "test commit"
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# Running pre-commit hook...
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# >> Updating R documentation...
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# >> done.
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# >>
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# >> Updating semantic versioning and date...
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# >> - latest tag is 'v1.8.1', with 26 previous commits
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# >> - testpkg pkg version set to 1.8.1.9027
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# >> - updated DESCRIPTION
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# >> - updated NEWS.md
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# >>
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# [main 300b93e] test commit
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# 3 files changed, 3 insertions(+), 4 deletions(-)
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```
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### Website Generation
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### Commiting Changes
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## Updating the AMR Package
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### Update EUCAST/CLSI Guidelines
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### Update the Microbial Taxonomy
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### Update the Antimicrobial Agents
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### Add or Update a Language for Translation
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For the most ideal workflow, please fork this repository and make the changes in your own forked repository. Afterwards, please create a Pull Request. If you are unfamiliar with these terms, no problem at all! Then please send us the edited files by email or any way you prefer.
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The repository file [`data-raw/translations.tsv`](https://github.com/msberends/AMR/blob/main/developer-guideline.md) contains all translations. This file will be read by all functions where a translated output can be desired, like all `mo_*` functions (such as `mo_name()`, `mo_gramstain()`, `mo_type()`, etc.) and ``ab_*` functions (such as `ab_name()`, `ab_group()`, etc.).
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1. To **add** a translation, edit `data-raw/translations.tsv` (you can copy the contains to MS Excel for convenience and paste the contents back later), add a column where the new column name is a [ISO 639-1 language code](https://en.wikipedia.org/wiki/List_of_ISO_639-1_codes) (such as `en` for English, `de` for German and `es` for Spanish) and put in the new column all translated text from the first column.\
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\
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To **update** a translation, open `data-raw/translations.tsv` and save it with the language updates.
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2. Set the current working directory to the AMR package root folder (either by opening the AMR package as RStudio project, or by setting the working directory with `setwd()`).
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3. Run `source("data-raw/_language_update.R)"` to update the internal package data. If you have the `roxygen2` package installed, this script automatically updates the package documentation as well.
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Many thanks for your contribution!
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