Update dev-notes.rst #5 #11

draeger-lab · Jul 11, 2024 · 5ec95a0 · 5ec95a0
1 parent 8e8a0c4
commit 5ec95a0
Showing 1 changed file with 13 additions and 11 deletions.
diff --git 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 <https://refinegems.readthedocs.io/en/latest/development.html>`__.
 
 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