From e095611d7bf28705030d3f9a1fd015baa39681fb Mon Sep 17 00:00:00 2001
From: Mariya Goliyad <mgoliyad1@dt-login03.delta.ncsa.illinois.edu>
Date: Sun, 26 Apr 2026 18:59:47 -0500
Subject: [PATCH 1/4] fix CI

---
 .github/{ => workflows}/test.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)
 rename .github/{ => workflows}/test.yml (94%)

diff --git a/.github/test.yml b/.github/workflows/test.yml
similarity index 94%
rename from .github/test.yml
rename to .github/workflows/test.yml
index c13f1f9..f4d63d9 100644
--- a/.github/test.yml
+++ b/.github/workflows/test.yml
@@ -2,9 +2,9 @@ name: Tests
 
 on:
   push:
-    branches: [main, master]
+    branches: [devel]
   pull_request:
-    branches: [main, master]
+    branches: [devel]
 
 jobs:
   test:

From e3d549be4b35954bcbd03a909df9f8b8278c502b Mon Sep 17 00:00:00 2001
From: Mariya Goliyad <mgoliyad1@dt-login03.delta.ncsa.illinois.edu>
Date: Sun, 26 Apr 2026 19:06:29 -0500
Subject: [PATCH 2/4] fixed CI error

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index f4d63d9..bf1bf8c 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -12,7 +12,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11"]
 
     steps:
       - uses: actions/checkout@v4

From 3b43b45fbd22e72597678c6a856eaad0b097591a Mon Sep 17 00:00:00 2001
From: Mariya Goliyad <mgoliyad1@dt-login03.delta.ncsa.illinois.edu>
Date: Sun, 26 Apr 2026 19:08:31 -0500
Subject: [PATCH 3/4] fixed error for ruff check

---
 workflows/sgdes/sgdes_workflow.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/workflows/sgdes/sgdes_workflow.py b/workflows/sgdes/sgdes_workflow.py
index 962c5ad..46b7b2f 100644
--- a/workflows/sgdes/sgdes_workflow.py
+++ b/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)

From b7bacc274155879e007abfaa95abcad056f13fad Mon Sep 17 00:00:00 2001
From: Mariya Goliyad <mgoliyad1@dt-login03.delta.ncsa.illinois.edu>
Date: Sun, 26 Apr 2026 19:12:40 -0500
Subject: [PATCH 4/4] fix for pytest

---
 pyproject.toml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index fde6b59..8d570a2 100644
--- a/pyproject.toml
+++ b/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