Merge pull request #75 from GavinHuttley/develop

Remove source of error on Linux

noxfile.py

@@ -14,10 +14,3 @@ def test(session):
         "-x",
         *session.posargs,
     )
-
-
-@nox.session(python=[f"3.{v}" for v in _py_versions])
-def test_fast(session):
-    session.install(".[test]")
-    session.chdir("tests")
-    session.run("pytest", "-s", "-x", "-m", "not internet and not slow")

pyproject.toml

@@ -23,7 +23,6 @@ dependencies = ["blosc2",
         "numpy",
         "trogon",
         "unsync",
-        "wakepy>0.7",
         ]
 classifiers = [
         "Development Status :: 5 - Production/Stable",

src/ensembl_lite/_util.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import contextlib
 import functools
 import os
 import pathlib
@@ -371,3 +372,8 @@ def sanitise_stableid(stableid: str) -> str:
     this function removes redundant biotype component.
     """
     return _biotypes.sub("", stableid)
+
+
+@contextlib.contextmanager
+def fake_wake(*args, **kwargs):
+    yield

src/ensembl_lite/cli.py

@@ -5,7 +5,12 @@
 from collections import defaultdict
 
 import click
-import wakepy.keep
+
+
+try:
+    import wakepy.keep.running as keep_running
+except ImportError:
+    from ensembl_lite._util import fake_wake as keep_running
 
 from rich.progress import track
 from trogon import tui
@@ -242,7 +247,7 @@ def download(configpath, debug, verbose):
         print(config.species_dbs)
 
     config.write()
-    with wakepy.keep.running():
+    with keep_running():
         download_species(config, debug, verbose)
         download_homology(config, debug, verbose)
         download_aligns(config, debug, verbose)
@@ -273,7 +278,7 @@ def install(download, num_procs, force_overwrite, verbose):
 
     config.install_path.mkdir(parents=True, exist_ok=True)
     write_installed_cfg(config)
-    with wakepy.keep.running():
+    with keep_running():
         local_install_genomes(
             config, force_overwrite=force_overwrite, max_workers=num_procs
         )