latch 2.39.0.dev30__tar.gz → 2.39.0.dev32__tar.gz

{latch-2.39.0.dev30/latch.egg-info → latch-2.39.0.dev32}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: latch
-Version: 2.39.0.dev30
+Version: 2.39.0.dev32
 Summary: The Latch SDK
 Author-email: kenny@latch.bio
 Classifier: Programming Language :: Python :: 3.8

{latch-2.39.0.dev30 → latch-2.39.0.dev32/latch.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: latch
-Version: 2.39.0.dev30
+Version: 2.39.0.dev32
 Summary: The Latch SDK
 Author-email: kenny@latch.bio
 Classifier: Programming Language :: Python :: 3.8

{latch-2.39.0.dev30 → latch-2.39.0.dev32}/latch_cli/extras/common/serialize.py

@@ -348,6 +348,9 @@ def serialize(
 
         registrable_entities.append(x.to_flyte_idl())
 
+    click.echo("\x1b[0K", nl=False)
+    click.secho("Done. \x1b[?25h", italic=True)
+
     click.secho("\nSerializing workflow entities", bold=True)
 
     persist_registrable_entities(registrable_entities, output_dir)

{latch-2.39.0.dev30 → latch-2.39.0.dev32}/latch_cli/extras/nextflow/file_persistence.py

@@ -2,6 +2,7 @@ import os
 import shutil
 from pathlib import Path
 from typing import Dict, List, Optional, Set, Union
+from urllib.parse import urlparse
 
 import click
 import gql
@@ -59,7 +60,14 @@ def _extract_paths(parameter: JSONValue, res: List[Path]):
     if k == "path":
         assert isinstance(v, str)
 
-        res.append(Path(v).absolute().relative_to(Path.home()))
+        parsed = urlparse(v)
+        if parsed.scheme == "latch":
+            p = LPath(v).download()
+            res.append(p)
+            parameter[k] = str(p)
+        elif parsed.scheme == "":
+            res.append(Path(v).absolute().relative_to(Path.home()))
+
     elif k == "list":
         assert isinstance(v, List)
 

{latch-2.39.0.dev30 → latch-2.39.0.dev32}/latch_cli/extras/nextflow/tasks/base.py

@@ -46,9 +46,9 @@ class NextflowBaseTask(PythonAutoContainerTask[Pod]):
         branches: Dict[str, bool],
         wf: NextflowWorkflow,
         nf_task_type: NFTaskType,
-        # todo(ayush): expose / infer these somehow
-        cpu: float = 0.5,
-        memory: float = 1,
+        # ayush: 0.5/1 is too small and stuff starts taking a while to run
+        cpu: float = 1,
+        memory: float = 2,
     ):
         self.id = id
         self.wf = wf

{latch-2.39.0.dev30 → latch-2.39.0.dev32}/latch_cli/extras/nextflow/tasks/operator.py

@@ -115,6 +115,8 @@ class NextflowOperatorTask(NextflowBaseTask):
             "/root/nextflow",
             "run",
             str(nf_script_path_in_container),
+            "-lib",
+            "lib",
         ]
 
         for flag, val in self.wf.flags_to_params.items():
@@ -190,6 +192,7 @@ class NextflowOperatorTask(NextflowBaseTask):
                         [{', '.join([f"str({x})" if x.startswith("wf_") else repr(x) for x in run_task_entrypoint])}],
                         env={{
                             **os.environ,
+                            "LATCH_CONFIG_DIR_OVERRIDE": str(Path.cwd()),
                             "LATCH_EXPRESSION": {repr(self.statement)},
                             "LATCH_RETURN": {repr(json.dumps(self.ret))},
                             "LATCH_PARAM_VALS": json.dumps(channel_vals),

{latch-2.39.0.dev30 → latch-2.39.0.dev32}/latch_cli/extras/nextflow/tasks/process.py

@@ -116,6 +116,8 @@ class NextflowProcessTask(NextflowBaseTask):
             "/root/nextflow",
             "run",
             str(nf_script_path_in_container),
+            "-lib",
+            "lib",
         ]
 
         if self.execution_profile is not None:
@@ -171,6 +173,7 @@ class NextflowProcessTask(NextflowBaseTask):
                     [{','.join([f"str({x})" if x.startswith("wf_") else repr(x) for x in run_task_entrypoint])}],
                     env={{
                         **os.environ,
+                        "LATCH_CONFIG_DIR_OVERRIDE": str(Path.cwd()),
                         "LATCH_EXPRESSION": {repr(self.statement)},
                         "LATCH_RETURN": {repr(json.dumps(self.ret))},
                         "LATCH_PARAM_VALS": json.dumps(channel_vals),

{latch-2.39.0.dev30 → latch-2.39.0.dev32}/setup.py

@@ -13,7 +13,7 @@ if cur_ver < (3, 8) or cur_ver > (3, 11):
 
 setup(
     name="latch",
-    version="v2.39.0.dev30",
+    version="v2.39.0.dev32",
     author_email="kenny@latch.bio",
     description="The Latch SDK",
     packages=find_packages(),