fix CI

.github/test.yml → .github/workflows/test.yml

@@ -2,17 +2,17 @@ name: Tests
 
 on:
   push:
-    branches: [main, master]
+    branches: [devel]
   pull_request:
-    branches: [main, master]
+    branches: [devel]
 
 jobs:
   test:
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11"]
 
     steps:
       - uses: actions/checkout@v4

pyproject.toml

@@ -77,7 +77,9 @@ dev = [
     "pytest>=7.0.0",
     "pytest-asyncio>=0.21.0",
     "pytest-cov>=4.0.0",
+    "anyio>=4.0.0",
     "ruff>=0.1.0",
+    "numpy>=1.24.0,<2.0.0",
 ]
 
 # Documentation

workflows/sgdes/sgdes_workflow.py

@@ -380,8 +380,11 @@ async def _run_des(self, tasks, **kwargs) -> None:
         #   single-node → DES_TMPDIR (/tmp): fast local I/O, ~10 s/createdb step
         #   multi-node  → None (Lustre):      shared across nodes, ~27-130 s/step
         # See run_workflow.py for the full rationale.
-        _workdir_base = self.des_workdir_base if self.des_workdir_base is not None \
+        _workdir_base = (
+            self.des_workdir_base
+            if self.des_workdir_base is not None
             else os.path.dirname(des_fasta)
+        )
         workdir = tempfile.mkdtemp(prefix="fsim_", dir=_workdir_base)
 
         # foldseek_search's internal scratch stays on node-local /tmp regardless.
@@ -501,6 +504,7 @@ def my_initializer(dom, batch_size, random_state):
                 os.remove(cand_fa)
                 os.remove(out_tsv)
                 import glob as _glob
+
                 for _f in _glob.glob(f"{cand_db}*"):
                     try:
                         os.remove(_f)