latch 2.41.3.dev2__tar.gz → 2.41.3.dev4__tar.gz

{latch-2.41.3.dev2/latch.egg-info → latch-2.41.3.dev4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: latch
-Version: 2.41.3.dev2
+Version: 2.41.3.dev4
 Summary: The Latch SDK
 Author-email: kenny@latch.bio
 Classifier: Programming Language :: Python :: 3.8

{latch-2.41.3.dev2 → latch-2.41.3.dev4}/latch/resources/tasks.py

@@ -518,7 +518,7 @@ def nextflow_runtime_task(cpu: int, memory: int):
         },
         pod_spec=V1PodSpec(
             runtime_class_name="sysbox-runc",
-            service_account_name="rahul-test",
+            automount_service_account_token=True,
             containers=[primary_container],
             volumes=[
                 V1Volume(

{latch-2.41.3.dev2 → latch-2.41.3.dev4}/latch/types/directory.py

@@ -114,10 +114,10 @@ class LatchDir(FlyteDirectory):
         self._path_generated = False
 
         if is_valid_url(self.path) and remote_path is None:
-            self._raw_remote_path = path
+            self._raw_remote_path = str(path)
             self._remote_directory = self.path
         else:
-            self._raw_remote_path = remote_path
+            self._raw_remote_path = str(remote_path)
             self._remote_directory = None if remote_path is None else str(remote_path)
 
         if kwargs.get("downloader") is not None:

{latch-2.41.3.dev2 → latch-2.41.3.dev4}/latch/types/file.py

@@ -77,8 +77,10 @@ class LatchFile(FlyteFile):
         self._path_generated = False
 
         if is_valid_url(self.path) and remote_path is None:
+            self._raw_remote_path = str(path)
             self._remote_path = str(path)
         else:
+            self._raw_remote_path = str(remote_path)
             self._remote_path = None if remote_path is None else str(remote_path)
 
         if kwargs.get("downloader") is not None:

{latch-2.41.3.dev2 → latch-2.41.3.dev4/latch.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: latch
-Version: 2.41.3.dev2
+Version: 2.41.3.dev4
 Summary: The Latch SDK
 Author-email: kenny@latch.bio
 Classifier: Programming Language :: Python :: 3.8

{latch-2.41.3.dev2 → latch-2.41.3.dev4}/latch_cli/nextflow/dependencies.py

@@ -37,7 +37,8 @@ def download_nf_jars(pkg_root: Path):
     s3_resource = boto3.resource("s3")
     bucket = s3_resource.Bucket("latch-public")
 
-    objects = list(bucket.objects.filter(Prefix=".nextflow/"))
+    subdir = "nextflow-v2/"
+    objects = list(bucket.objects.filter(Prefix=f"{subdir}.nextflow/"))
 
     click.secho("  Downloading Nextflow binaries: \x1b[?25l", italic=True, nl=False)
 
@@ -49,7 +50,8 @@ def download_nf_jars(pkg_root: Path):
                 url = urljoin(
                     "https://latch-public.s3.us-west-2.amazonaws.com/", obj.key
                 )
-                obj_path = pkg_root / ".latch" / obj.key
+                obj_path = pkg_root / ".latch" / obj.key[len(subdir) :]
+                print(obj_path)
 
                 exec.submit(_do_download, url, obj_path, len(objects), counter, lock)
 
@@ -58,18 +60,6 @@ def download_nf_jars(pkg_root: Path):
 
 
 def ensure_nf_dependencies(pkg_root: Path, *, force_redownload: bool = False):
-    try:
-        subprocess.run(["java", "--version"], check=True, capture_output=True)
-    except (subprocess.CalledProcessError, FileNotFoundError) as e:
-        click.secho(
-            dedent("""\
-            Java is not installed - this is a requirement to run Nextflow.
-            Please install Java and try again.
-            """),
-            fg="red",
-        )
-        raise click.exceptions.Exit(1) from e
-
     nf_executable = pkg_root / ".latch" / "bin" / "nextflow"
     nf_jars = pkg_root / ".latch" / ".nextflow"
 
@@ -80,7 +70,7 @@ def ensure_nf_dependencies(pkg_root: Path, *, force_redownload: bool = False):
 
     if not nf_executable.exists():
         res = tinyrequests.get(
-            "https://latch-public.s3.us-west-2.amazonaws.com/nextflow"
+            "https://latch-public.s3.us-west-2.amazonaws.com/nextflow-v2/nextflow"
         )
         nf_executable.parent.mkdir(parents=True, exist_ok=True)
 

{latch-2.41.3.dev2 → latch-2.41.3.dev4}/latch_cli/nextflow/workflow.py

@@ -7,7 +7,7 @@ from typing import Any, List, Optional, Tuple
 import click
 
 import latch.types.metadata as metadata
-from latch.types.directory import LatchDir
+from latch.types.directory import LatchDir, LatchOutputDir
 from latch.types.file import LatchFile
 from latch_cli.snakemake.config.utils import get_preamble, type_repr
 from latch_cli.snakemake.utils import reindent
@@ -176,6 +176,16 @@ def generate_nextflow_workflow(
         if param.default is not None:
             if isinstance(param.default, Enum):
                 defaults.append((sig, param.default))
+            elif param.type in {LatchDir, LatchFile}:
+                defaults.append((
+                    sig,
+                    f"{param.type.__name__}('{param.default._raw_remote_path}')",
+                ))
+            elif param.type is LatchOutputDir:
+                defaults.append((
+                    sig,
+                    f"LatchOutputDir('{param.default._raw_remote_path}')",
+                ))
             else:
                 defaults.append((sig, repr(param.default)))
         else:
@@ -195,7 +205,7 @@ def generate_nextflow_workflow(
         workflow_func_name=identifier_from_str(workflow_name),
         nf_script=nf_script.resolve().relative_to(pkg_root.resolve()),
         param_signature_with_defaults=", ".join(
-            no_defaults + [f"{name}={val}" for name, val in defaults]
+            no_defaults + [f"{name} = {val}" for name, val in defaults]
         ),
         param_signature=", ".join(no_defaults + [name for name, _ in defaults]),
         param_args=", ".join(

{latch-2.41.3.dev2 → latch-2.41.3.dev4}/setup.py

@@ -13,7 +13,7 @@ if cur_ver < (3, 8) or cur_ver > (3, 11):
 
 setup(
     name="latch",
-    version="v2.41.3.dev2",
+    version="v2.41.3.dev4",
     author_email="kenny@latch.bio",
     description="The Latch SDK",
     packages=find_packages(),