fix: adapt to API changes in Snakemake 8

.github/workflows/ci.yml

@@ -13,19 +13,24 @@ jobs:
       - name: Check out the code
         uses: actions/checkout@v3
 
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+
       - name: Install poetry
-        run: pipx install poetry
+        run: pip install poetry
 
       - name: Determine dependencies
         run: poetry lock
 
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.9"
+          python-version: "3.11"
           cache: poetry
 
-      - name: Install Dependencies using Poetry
-        run: poetry install
+      - name: Install dependencies
+        run: |
+          poetry install
 
       - name: Check formatting
         run: poetry run black --check .
@@ -36,19 +41,24 @@ jobs:
       - name: Check out the code
         uses: actions/checkout@v3
 
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+
       - name: Install poetry
-        run: pipx install poetry
+        run: pip install poetry
 
       - name: Determine dependencies
         run: poetry lock
 
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.9"
+          python-version: "3.11"
           cache: poetry
 
-      - name: Install Dependencies using Poetry
-        run: poetry install
+      - name: Install dependencies
+        run: |
+          poetry install
 
       - name: Check code
         run: poetry run flake8
@@ -68,15 +78,19 @@ jobs:
 
       - uses: koesterlab/setup-slurm-action@v1
 
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+
       - name: Install poetry
-        run: pipx install poetry
+        run: pip install poetry
 
       - name: Determine dependencies
         run: poetry lock
 
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.9"
+          python-version: "3.11"
           cache: poetry
 
       - name: Install dependencies

pyproject.toml

@@ -10,10 +10,10 @@ authors = [
 readme = "README.md"
 
 [tool.poetry.dependencies]
-python = "^3.9"
-snakemake-interface-common = "^1.12.0"
-snakemake-interface-executor-plugins = "^6.0.0"
-snakemake-executor-plugin-slurm-jobstep = "^0.1.0"
+python = "^3.11"
+snakemake-interface-common = "^1.13.0"
+snakemake-interface-executor-plugins = "^7.0.0"
+snakemake-executor-plugin-slurm-jobstep = "^0.1.4"
 throttler = "^1.2.2"
 
 [tool.poetry.group.dev.dependencies]

snakemake_executor_plugin_slurm/__init__.py

@@ -36,30 +36,19 @@
     # filesystem (True) or not (False).
     # This is e.g. the case for cloud execution.
     implies_no_shared_fs=False,
+    pass_default_storage_provider_args=True,
+    pass_default_resources_args=True,
+    pass_envvar_declarations_to_cmd=False,
+    auto_deploy_default_storage_provider=False,
+    # wait a bit until slurmdbd has job info available
+    init_seconds_before_status_checks=40
 )
 
 
 # Required:
 # Implementation of your executor
 class Executor(RemoteExecutor):
-    def __init__(
-        self,
-        workflow: WorkflowExecutorInterface,
-        logger: LoggerExecutorInterface,
-    ):
-        super().__init__(
-            workflow,
-            logger,
-            # configure behavior of RemoteExecutor below
-            # whether arguments for setting the remote provider shall  be passed to jobs
-            pass_default_storage_provider_args=True,
-            # whether arguments for setting default resources shall be passed to jobs
-            pass_default_resources_args=True,
-            # whether environment variables shall be passed to jobs
-            pass_envvar_declarations_to_cmd=False,
-            # wait a bit until slurmdbd has job info available
-            init_seconds_before_status_checks=40,
-        )
+    def __post_init__(self):
         self.run_uuid = str(uuid.uuid4())
         self._fallback_account_arg = None
         self._fallback_partition = None