Merge pull request #124 from GavinHuttley/develop

MAINT: style and doc update

README.md

@@ -193,7 +193,12 @@ $ elt install -d downloaded_data -np 2
 
 ## Interrogating the data
 
-The full list of subcommands is shown below. You can get help on individual subcommands by running `elt <subcommand>` in the terminal.
+We provide a conventional command line interface for querying the data with subcommands.
+
+<details>
+ <summary>The full list of subcommands</summary>
+
+ You can get help on individual subcommands by running `elt <subcommand>` in the terminal.
 
  <!-- [[[cog
  import cog
@@ -230,4 +235,6 @@ The full list of subcommands is shown below. You can get help on individual subc
  ```
  <!-- [[[end]]] -->
 
+</details>
+
 We also provide an experiment terminal user interface (TUI) that allows you to explore the data in a more interactive way. This is invoked with the `tui` subcommand.

src/ensembl_lite/_genomedb.py

@@ -541,7 +541,7 @@ def get_stableid_prefixes(records: typing.Sequence[EnsemblGffRecord]) -> set[str
 
 
 def make_annotation_db(
- src_dest: tuple[pathlib.Path, pathlib.Path]
+ src_dest: tuple[pathlib.Path, pathlib.Path],
 ) -> tuple[str, set[str]]:
  """convert gff3 file into a EnsemblGffDb
 

tests/test_genomedb.py

@@ -290,7 +290,6 @@ def test_has_of_seqsdata(h5_genome):
 
 
 def test_tidying_stableids_in_gff3():
-
  orig = (
  "ID=Transcript:ENST00000461467;Parent=Gene:ENSG00000237613;Name=FAM138A-202;bio"
  )