latch 2.45.2.dev2__tar.gz → 2.45.2.dev3__tar.gz

{latch-2.45.2.dev2/latch.egg-info → latch-2.45.2.dev3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: latch
-Version: 2.45.2.dev2
+Version: 2.45.2.dev3
 Summary: The Latch SDK
 Author-email: kenny@latch.bio
 Classifier: Programming Language :: Python :: 3.8

{latch-2.45.2.dev2 → latch-2.45.2.dev3/latch.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: latch
-Version: 2.45.2.dev2
+Version: 2.45.2.dev3
 Summary: The Latch SDK
 Author-email: kenny@latch.bio
 Classifier: Programming Language :: Python :: 3.8

{latch-2.45.2.dev2 → latch-2.45.2.dev3}/latch_cli/nextflow/workflow.py

@@ -60,17 +60,19 @@ def initialize() -> str:
 
 {preambles}
 
-{samplesheet_constructors}
+{samplesheet_funs}
 
 @nextflow_runtime_task(cpu={cpu}, memory={memory})
 def nextflow_runtime(pvc_name: str, {param_signature}) -> None:
     try:
         shared_dir = Path("/nf-workdir")
 
+{samplesheet_constructors}
+
         shutil.copytree(
             Path("/root"),
             shared_dir,
-            ignore=lambda src, names: ["latch", ".latch"],
+            ignore=lambda src, names: ["latch", ".latch", "nextflow", ".nextflow"],
             ignore_dangling_symlinks=True,
             dirs_exist_ok=True,
         )
@@ -95,12 +97,13 @@ def nextflow_runtime(pvc_name: str, {param_signature}) -> None:
             ],
             env=env,
             check=True,
+            cwd=str(shared_dir),
         )
     except subprocess.CalledProcessError:
         remote = LPath(urljoins("{remote_output_dir}", _get_execution_name(), "nextflow.log"))
         print()
         print(f"Uploading .nextflow.log to {{remote.path}}")
-        remote.upload_from(Path("/root/.nextflow.log"))
+        remote.upload_from(shared_dir / ".nextflow.log")
         raise
     finally:
         token = os.environ.get("FLYTE_INTERNAL_EXECUTION_ID")
@@ -172,7 +175,8 @@ def generate_nextflow_workflow(
     flags = []
     defaults: List[Tuple[str, str]] = []
     no_defaults: List[str] = []
-    preambles: List[str] = []
+    preambles: set[str] = set()
+    samplesheet_funs: List[str] = []
     samplesheet_constructors: List[str] = []
     for param_name, param in parameters.items():
         sig = f"{param_name}: {type_repr(param.type)}"
@@ -195,7 +199,7 @@ def generate_nextflow_workflow(
             no_defaults.append(sig)
 
         if param.samplesheet:
-            samplesheet_constructors.append(
+            samplesheet_funs.append(
                 reindent(
                     f"""
                     {param_name}_construct_samplesheet = metadata._nextflow_metadata.parameters[{repr(param_name)}].samplesheet_constructor
@@ -204,10 +208,17 @@ def generate_nextflow_workflow(
                 ),
             )
 
+            samplesheet_constructors.append(
+                reindent(
+                    f"{param_name}_samplesheet ="
+                    f" {param_name}_construct_samplesheet({param_name})",
+                    2,
+                ),
+            )
+
             flags.append(
                 reindent(
-                    f"*get_flag({repr(param_name)},"
-                    f" {param_name}_construct_samplesheet({param_name}))",
+                    f"*get_flag({repr(param_name)}, {param_name}_samplesheet)",
                     4,
                 )
             )
@@ -215,8 +226,8 @@ def generate_nextflow_workflow(
             flags.append(reindent(f"*get_flag({repr(param_name)}, {param_name})", 4))
 
         preamble = get_preamble(param.type)
-        if len(preamble) > 0:
-            preambles.append(preamble)
+        if len(preamble) > 0 and preamble not in preambles:
+            preambles.add(preamble)
 
     if metadata._nextflow_metadata.output_dir is None:
         output_dir = "latch:///nextflow_outputs"
@@ -238,7 +249,8 @@ def generate_nextflow_workflow(
         execution_profile=(
             execution_profile if execution_profile is not None else "standard"
         ),
-        preambles="\n\n".join(preambles),
+        preambles="\n\n".join(list(preambles)),
+        samplesheet_funs="\n".join(samplesheet_funs),
         samplesheet_constructors="\n".join(samplesheet_constructors),
         cpu=resources.cpus,
         memory=resources.memory,

{latch-2.45.2.dev2 → latch-2.45.2.dev3}/setup.py

@@ -13,7 +13,7 @@ if cur_ver < (3, 8) or cur_ver > (3, 11):
 
 setup(
     name="latch",
-    version="v2.45.2.dev2",
+    version="v2.45.2.dev3",
     author_email="kenny@latch.bio",
     description="The Latch SDK",
     packages=find_packages(),