Merge pull request #100 from GavinHuttley/develop

ENH: support specifying downloading homologies in config

src/ensembl_lite/_config.py

@@ -27,6 +27,7 @@ class Config:
     species_dbs: dict[str, list[str]]
     align_names: Iterable[str]
     tree_names: Iterable[str]
+    homologies: bool
 
     def update_species(self, species: dict[str, list[str]]):
         if not species:
@@ -210,7 +211,7 @@ def read_config(config_path) -> Config:
     install_path = (
         pathlib.Path(parser.get("local path", "install_path")).expanduser().absolute()
     )
-
+    homologies = parser.has_option("compara", "homologies")
     species_dbs = {}
     get_option = parser.get
     align_names = []
@@ -248,4 +249,5 @@ def read_config(config_path) -> Config:
         species_dbs=species_dbs,
         align_names=align_names,
         tree_names=tree_names,
+        homologies=homologies,
     )

src/ensembl_lite/_download.py

@@ -154,7 +154,7 @@ def __call__(self, name: str) -> bool:
 
 def download_homology(config: Config, debug: bool, verbose: bool):
     """downloads tsv homology files for each genome"""
-    if not any((config.align_names, config.tree_names)):
+    if not config.homologies:
         return
 
     site_map = get_site_map(config.host)

src/ensembl_lite/data/sample.cfg

@@ -13,4 +13,6 @@ db=core
 db=core
 [compara]
 align_names=10_primates.epo
-tree_names=10_primates_EPO_default.nh
+tree_names=10_primates_EPO_default.nh
+# if you want homology data, keep the following line
+homologies =