save state

Signed-off-by: Ayush Kamat <[email protected]>

Justfile

@@ -1,7 +1,7 @@
 # Setup
 
 install:
-  uv sync
+  uv sync --group dev --group docs
 
 # Packaging
 
@@ -16,8 +16,8 @@ publish:
 # Testing
 
 test:
-  export TEST_TOKEN=$(cat ~/.latch/token) &&\
-    pytest -s tests
+  export TEST_TOKEN=$(cat ~/.latch/token)
+  pytest -s
 
 # Docs
 

pyproject.toml

@@ -12,7 +12,7 @@ include = ["src/**/*.py", "src/latch_cli/services/init/*"]
 
 [project]
 name = "latch"
-version = "2.54.0.a3"
+version = "2.54.0.a8"
 description = "The Latch SDK"
 authors = [{ name = "Kenny Workman", email = "[email protected]" }]
 maintainers = [
@@ -34,13 +34,13 @@ dependencies = [
   "scp>=0.14.0",
   "boto3>=1.26.0",
   "tqdm>=4.63.0",
-  "lytekit==0.15.13",
+  "lytekit==0.15.14",
   "lytekitplugins-pods==0.6.2",
   "typing-extensions>=4.12.0",
   "apscheduler>=3.10.0",
-  "gql==3.4.0",
+  "gql>=3.5.0,<4.0.0",
   "graphql-core==3.2.3",
-  "requests-toolbelt==0.10.1",
+  "requests-toolbelt>=1.0.0,<2.0.0",
   "python-dateutil>=2.8",
   "GitPython==3.1.40",
 
@@ -98,11 +98,10 @@ docs = [
 ]
 
 [tool.ruff]
+line-length = 100
 target-version = "py39"
 
 [tool.ruff.lint]
-preview = true
-
 pydocstyle = { convention = "google" }
 extend-select = [
   "F",
@@ -171,6 +170,9 @@ ignore = [
 
   "ANN101",
   "ANN102",
+  "ANN201",
+
+  "D202",
 
   "E402",
   "E501",

src/latch/resources/tasks.py

@@ -296,8 +296,7 @@ def _get_small_pod() -> Pod:
             )
         },
         pod_spec=V1PodSpec(
-            runtime_class_name="sysbox-runc",
-            containers=[primary_container],
+            runtime_class_name="sysbox-runc", containers=[primary_container]
         ),
         primary_container_name="primary",
     )
@@ -517,11 +516,7 @@ class _NGConfig:
 max_storage_gb_ish = int(max_storage_gib * Units.GiB / Units.GB)
 
 
-def _custom_task_config(
-    cpu: int,
-    memory: int,
-    storage_gib: int,
-) -> Pod:
+def _custom_task_config(cpu: int, memory: int, storage_gib: int) -> Pod:
     target_ng = None
     for ng in taint_data:
         if (
@@ -591,10 +586,7 @@ def custom_task(
     """
     if callable(cpu) or callable(memory) or callable(storage_gib):
         task_config = DynamicTaskConfig(
-            cpu=cpu,
-            memory=memory,
-            storage=storage_gib,
-            pod_config=_get_small_pod(),
+            cpu=cpu, memory=memory, storage=storage_gib, pod_config=_get_small_pod()
         )
         return functools.partial(task, task_config=task_config, timeout=timeout)
 
@@ -627,3 +619,27 @@ def nextflow_runtime_task(cpu: int, memory: int, storage_gib: int = 50):
     ]
 
     return functools.partial(task, task_config=task_config)
+
+
+def snakemake_runtime_task(*, cpu: int, memory: int, storage_gib: int = 50):
+    task_config = _custom_task_config(cpu, memory, storage_gib)
+
+    task_config.pod_spec.automount_service_account_token = True
+
+    assert len(task_config.pod_spec.containers) == 1
+    task_config.pod_spec.containers[0].volume_mounts = [
+        V1VolumeMount(mount_path="/snakemake-workdir", name="snakemake-workdir")
+    ]
+
+    task_config.pod_spec.volumes = [
+        V1Volume(
+            name="snakemake-workdir",
+            persistent_volume_claim=V1PersistentVolumeClaimVolumeSource(
+                # this value will be injected by flytepropeller
+                # ayush: this is also used by snakemake bc why not
+                claim_name="nextflow-pvc-placeholder"
+            ),
+        )
+    ]
+
+    return functools.partial(task, task_config=task_config)

src/latch/types/glob.py

@@ -20,7 +20,7 @@ def file_glob(
     represented by the `remote_directory`.
 
     Args:
-        pattern: A glob pattern to match a set of files, eg. '\*.py'. Will
+        pattern: A glob pattern to match a set of files, eg. '*.py'. Will
             resolve paths with respect to the working directory of the caller.
         remote_directory: A valid latch URL pointing to a directory, eg.
             latch:///foo. This _must_ be a directory and not a file.