news: use top level headings

NEWS.md

@@ -1,51 +1,51 @@
-## OmnipathR v3.2.0
+# OmnipathR v3.2.0
 
 + New resource: PrePPI
 + Configuration option to completely disable logging to file
 + New vignettes: Path reconstruction, and Bioconductor 2021 Workshop
 + Many minor bugfixes and improvements
 
-## OmnipathR v2.99.19 (v3.0.0)
+# OmnipathR v2.99.19 (v3.0.0)
 
 + NicheNet pipeline works
 + Fixed an error which resulted value 1 in the `n_references` columns
 even for records without references
 
-## OmnipathR v2.99.17
+# OmnipathR v2.99.17
 
 + Improved quality filtering of intercell networks
 
-## OmnipathR v2.99.16
+# OmnipathR v2.99.16
 
 + Improved API for translate_ids
 + Quality filtering of intercell networks
 
-## OmnipathR v2.99.13
+# OmnipathR v2.99.13
 
 + Functions to access KEGG Pathways
 + More robust access to UniProt (in case of network failures)
 
-## OmnipathR v2.99.11
+# OmnipathR v2.99.11
 
 + Improved downloader backends
 
-## OmnipathR v2.99.8
+# OmnipathR v2.99.8
 
 + OBO parser
 + Gene Ontology access, functions to work with ontology trees
 + Database manager
 
-## OmnipathR v2.99.7
+# OmnipathR v2.99.7
 
 + New interactions query parameter: loops
 + Fixed many caching bugs
 
-## OmnipathR v2.99.6
+# OmnipathR v2.99.6
 
 + All downloaders attempt 3 times
 + New resources: Human Phenotype Ontology and Gene Ontology annotations
 
-## OmnipathR v2.99.0 (2021-03-08)
+# OmnipathR v2.99.0 (2021-03-08)
 
 + Many new resources besides OmniPath:
 BioPlex, ConsensusPathDB, EVEX, Guide to Pharmacology (IUPHAR/BPS),
@@ -61,35 +61,35 @@ certain length; extracting the giant component of a graph
 + Logging
 + Configuration handling
 
-## OmnipathR v1.99.0 (2020-10-03)
+# OmnipathR v1.99.0 (2020-10-03)
 
 + New tests
 + Many little bugfixes
 + Updated package metadata
 + Preparation for Bioconductor 3.12
 
-## OmnipathR v1.3.4 (2020-08-04)
+# OmnipathR v1.3.4 (2020-08-04)
 
 + License and password handling
 + Can be directed to different server by options
 
-## OmnipathR v1.3.1 (2020-06-05)
+# OmnipathR v1.3.1 (2020-06-05)
 
 + Addition of the package website.
 + Modification of the pdf vignette for an html one.
 + Major refactoring of functions.
 + Addition of the intercellular network function.
 + Modification for the intercellular categories.
 
-## OmnipathR v1.1.4 (2020-03-28)
+# OmnipathR v1.1.4 (2020-03-28)
 + Refactored the `import_annotations` method
 
-## OmnipathR v0.99.12 (2019-10-10)
+# OmnipathR v0.99.12 (2019-10-10)
 
 + Modification in the separation between genes within a complex (from dash
 to underscore)
 
-## OmnipathR v0.99.0 (2019-10-10)
+# OmnipathR v0.99.0 (2019-10-10)
 
 + Submitted to Bioconductor