diff --git a/docs/source/dev-notes.rst b/docs/source/dev-notes.rst index 6ab7af7..653a41d 100644 --- a/docs/source/dev-notes.rst +++ b/docs/source/dev-notes.rst @@ -8,22 +8,24 @@ Below you can find information on the currently available branches. If you plan to add a new feature or extension, please create your own branch, as to not implicate other developers. -**Main** +``main`` +^^^^^^^^ -The current version of the pipeline has been successfully tested on a *Klebsiella pneumoniae* and *Klebsiella oxytoca* genomes using -a *Klebsiella sp.* reference database and a *Klebsiella pneumoniae* template model. +Our first development release of ``SPECIMEN``. Please feel free to test and leave issues on GitHub if you encounter bugs or have suggestions. +The version in this release has as of yet only be tested on prokaryote genomes. .. note:: - The pipeline has yet to be tested on different species and specifically Eukarya, if it works without problem on those as well. + The pipeline has yet to be tested on different species and specifically Eukarya, if it works without problems on those as well. -**refinegems-integration** : ONGOING +``dev``: ONGOING +^^^^^^^^^^^^^^^^ -Branch for the integration of ``SPECIMEN``-functionalities into refineGEMS and vice versa. +Development branch. +Currently, features marked as future update throughout the documentation are worked on. -Integration done. Cleanup for first development release of ``SPECIMEN`` pending. - -**Further branches** +Further branches +^^^^^^^^^^^^^^^^ Currently, there are no more branches. @@ -35,12 +37,12 @@ More developer-relevant information can be found in the :code:`dev` folder on th Documentation Notes ------------------- -The documentation is generated based the Sphinx :code:`sphinx.ext.autodoc` extension. +The documentation is generated based on the Sphinx :code:`sphinx.ext.autodoc` extension. A mustache-file with additional formatting can be found in the :code:`dev` folder (ready to integrate in e.g. VSCode). For further information refer to the `refineGEMS documentation notes `__. Please annotate new functions with restructured text for them to be included into this documentation. -Furthermore, please use type setting for the functions, e.g.: +Furthermore, please use type hinting for the functions, e.g.: .. code-block:: python