diff --git a/.github/test.yml b/.github/workflows/test.yml similarity index 89% rename from .github/test.yml rename to .github/workflows/test.yml index c13f1f9..bf1bf8c 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: @@ -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 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 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)