latch 2.46.2__tar.gz → 2.46.2.dev1__tar.gz

{latch-2.46.2/latch.egg-info → latch-2.46.2.dev1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: latch
-Version: 2.46.2
+Version: 2.46.2.dev1
 Summary: The Latch SDK
 Author-email: kenny@latch.bio
 Classifier: Programming Language :: Python :: 3.8

{latch-2.46.2 → latch-2.46.2.dev1}/latch/resources/tasks.py

@@ -480,44 +480,23 @@ def custom_task(
 
 
 def nextflow_runtime_task(cpu: int, memory: int, storage_gib: int = 50):
-    primary_container = V1Container(name="primary")
-    resources = V1ResourceRequirements(
-        requests={
-            "cpu": str(cpu),
-            "memory": f"{memory}Gi",
-            "ephemeral-storage": f"{storage_gib}Gi",
-        },
-        limits={
-            "cpu": str(cpu),
-            "memory": f"{memory}Gi",
-            "ephemeral-storage": f"{storage_gib}Gi",
-        },
-    )
-    primary_container.resources = resources
-    volume_mounts = [V1VolumeMount(mount_path="/nf-workdir", name="nextflow-workdir")]
-    primary_container.volume_mounts = volume_mounts
-
-    task_config = Pod(
-        annotations={
-            "io.kubernetes.cri-o.userns-mode": (
-                "private:uidmapping=0:1048576:65536;gidmapping=0:1048576:65536"
-            )
-        },
-        pod_spec=V1PodSpec(
-            runtime_class_name="sysbox-runc",
-            automount_service_account_token=True,
-            containers=[primary_container],
-            volumes=[
-                V1Volume(
-                    name="nextflow-workdir",
-                    persistent_volume_claim=V1PersistentVolumeClaimVolumeSource(
-                        # this value will be injected by flytepropeller
-                        claim_name="nextflow-pvc-placeholder"
-                    ),
-                )
-            ],
-        ),
-        primary_container_name="primary",
-    )
+    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="/nf-workdir", name="nextflow-workdir")
+    ]
+
+    task_config.pod_spec.volumes = [
+        V1Volume(
+            name="nextflow-workdir",
+            persistent_volume_claim=V1PersistentVolumeClaimVolumeSource(
+                # this value will be injected by flytepropeller
+                claim_name="nextflow-pvc-placeholder"
+            ),
+        )
+    ]
 
     return functools.partial(task, task_config=task_config)

{latch-2.46.2 → latch-2.46.2.dev1/latch.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: latch
-Version: 2.46.2
+Version: 2.46.2.dev1
 Summary: The Latch SDK
 Author-email: kenny@latch.bio
 Classifier: Programming Language :: Python :: 3.8

{latch-2.46.2 → latch-2.46.2.dev1}/latch.egg-info/SOURCES.txt

@@ -112,13 +112,7 @@ latch_cli/services/execute/utils.py
 latch_cli/services/init/__init__.py
 latch_cli/services/init/init.py
 latch_cli/services/init/__pycache__/__init__.cpython-310.pyc
-latch_cli/services/init/__pycache__/__init__.cpython-311.pyc
-latch_cli/services/init/__pycache__/__init__.cpython-38.pyc
-latch_cli/services/init/__pycache__/__init__.cpython-39.pyc
 latch_cli/services/init/__pycache__/init.cpython-310.pyc
-latch_cli/services/init/__pycache__/init.cpython-311.pyc
-latch_cli/services/init/__pycache__/init.cpython-38.pyc
-latch_cli/services/init/__pycache__/init.cpython-39.pyc
 latch_cli/services/init/assemble_and_sort/.env
 latch_cli/services/init/assemble_and_sort/LICENSE
 latch_cli/services/init/assemble_and_sort/README.md
@@ -126,22 +120,18 @@ latch_cli/services/init/assemble_and_sort/__init__.py
 latch_cli/services/init/assemble_and_sort/assemble.py
 latch_cli/services/init/assemble_and_sort/sort.py
 latch_cli/services/init/assemble_and_sort/system-requirements.txt
-latch_cli/services/init/assemble_and_sort/__pycache__/__init__.cpython-310.pyc
 latch_cli/services/init/common/.dockerignore
 latch_cli/services/init/example_conda/__init__.py
 latch_cli/services/init/example_conda/conda_task.py
 latch_cli/services/init/example_conda/environment.yaml
-latch_cli/services/init/example_conda/__pycache__/__init__.cpython-310.pyc
 latch_cli/services/init/example_docker/__init__.py
 latch_cli/services/init/example_docker/task.py
-latch_cli/services/init/example_nf_integration/latch_metadata/__pycache__/__init__.cpython-311.pyc
 latch_cli/services/init/example_nfcore/Dockerfile
 latch_cli/services/init/example_nfcore/__init__.py
 latch_cli/services/init/example_nfcore/task.py
 latch_cli/services/init/example_r/__init__.py
 latch_cli/services/init/example_r/environment.R
 latch_cli/services/init/example_r/r_task.py
-latch_cli/services/init/example_r/__pycache__/__init__.cpython-310.pyc
 latch_cli/services/init/example_snakemake/Dockerfile
 latch_cli/services/init/example_snakemake/Snakefile
 latch_cli/services/init/example_snakemake/config.yaml
@@ -154,7 +144,6 @@ latch_cli/services/init/template/LICENSE
 latch_cli/services/init/template/README.md
 latch_cli/services/init/template/__init__.py
 latch_cli/services/init/template/task.py
-latch_cli/services/init/template/__pycache__/__init__.cpython-310.pyc
 latch_cli/services/register/__init__.py
 latch_cli/services/register/constants.py
 latch_cli/services/register/register.py

{latch-2.46.2 → latch-2.46.2.dev1}/latch_cli/nextflow/dependencies.py

@@ -12,7 +12,7 @@ from botocore.handlers import disable_signing
 
 from latch_cli import tinyrequests
 
-target_version = "v1.0.1"
+target_version = "v1.0.2"
 
 
 def _do_download(

{latch-2.46.2 → latch-2.46.2.dev1}/latch_cli/nextflow/workflow.py

@@ -117,6 +117,7 @@ def nextflow_runtime(pvc_name: str, {param_signature}) -> None:
         env = {{
             **os.environ,
             "NXF_HOME": "/root/.nextflow",
+            "NXF_OPTS": "-Xms{heap_memory}M -Xmx{memory}G -XX:ActiveProcessorCount={cpu}",
             "K8S_STORAGE_CLAIM_NAME": pvc_name,
             "NXF_DISABLE_CHECK_LATEST": "true",
         }}
@@ -126,18 +127,18 @@ def nextflow_runtime(pvc_name: str, {param_signature}) -> None:
             check=True,
             cwd=str(shared_dir),
         )
-    except subprocess.CalledProcessError:
+    finally:
         print()
 
-        name = _get_execution_name()
-        if name is None:
-            print("Skipping logs upload, failed to get execution name")
-        else:
-            remote = LPath(urljoins("{log_dir}", name, "nextflow.log"))
-            print(f"Uploading .nextflow.log to {{remote.path}}")
-            remote.upload_from(shared_dir / ".nextflow.log")
-
-        raise
+        nextflow_log = shared_dir / ".nextflow.log"
+        if nextflow_log.exists():
+            name = _get_execution_name()
+            if name is None:
+                print("Skipping logs upload, failed to get execution name")
+            else:
+                remote = LPath(urljoins("{log_dir}", name, "nextflow.log"))
+                print(f"Uploading .nextflow.log to {{remote.path}}")
+                remote.upload_from(nextflow_log)
 
 
 
@@ -310,6 +311,7 @@ def generate_nextflow_workflow(
         samplesheet_constructors="\n".join(samplesheet_constructors),
         cpu=resources.cpus,
         memory=resources.memory,
+        heap_memory=max(1, int(resources.memory * 1024 * 0.25)),
         storage_gib=resources.storage_gib,
         log_dir=log_dir,
     )

{latch-2.46.2 → latch-2.46.2.dev1}/setup.py

@@ -13,7 +13,7 @@ if cur_ver < (3, 8) or cur_ver > (3, 11):
 
 setup(
     name="latch",
-    version="v2.46.2",
+    version="v2.46.2.dev1",
     author_email="kenny@latch.bio",
     description="The Latch SDK",
     packages=find_packages(),