latch 2.39.0.dev33__tar.gz → 2.39.0.dev35__tar.gz

{latch-2.39.0.dev33/latch.egg-info → latch-2.39.0.dev35}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: latch
-Version: 2.39.0.dev33
+Version: 2.39.0.dev35
 Summary: The Latch SDK
 Author-email: kenny@latch.bio
 Classifier: Programming Language :: Python :: 3.8

{latch-2.39.0.dev33 → latch-2.39.0.dev35/latch.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: latch
-Version: 2.39.0.dev33
+Version: 2.39.0.dev35
 Summary: The Latch SDK
 Author-email: kenny@latch.bio
 Classifier: Programming Language :: Python :: 3.8

{latch-2.39.0.dev33 → latch-2.39.0.dev35}/latch_cli/centromere/ctx.py

@@ -266,7 +266,9 @@ class _CentromereCtx:
                     click.secho(
                         dedent(
                             "Make sure a `latch_metadata` package exists in the"
-                            " nextflow project root.",
+                            " nextflow project root."
+                            "\nYou can generate this package with the"
+                            "`latch generate-metadata --nextflow <pkg_root>` command.",
                         ),
                         fg="red",
                     )

{latch-2.39.0.dev33 → latch-2.39.0.dev35}/latch_cli/extras/nextflow/config.py

@@ -140,21 +140,21 @@ def generate_nf_metadata(
             from latch.types.file import LatchFile
             from latch.types.directory import LatchDir
 
-            __preambles__
+            ||preambles||
 
             # Import these into your `__init__.py` file:
             #
             # from .parameters import generated_parameters, file_metadata
 
             generated_parameters = {
-            __params__
+            ||params||
             }
 
             """,
             0,
         )
-        .replace("__preambles__", "".join(preambles))
-        .replace("__params__", "\n".join(params))
+        .replace("||preambles||", "".join(preambles))
+        .replace("||params||", "\n".join(params))
     )
 
     write_metadata(

{latch-2.39.0.dev33 → latch-2.39.0.dev35}/latch_cli/extras/nextflow/tasks/adapters.py

@@ -46,11 +46,11 @@ def get_dataclass_code(cls: Type[_IsDataclass]) -> str:
         rf"""
         @dataclass
         class {cls.__name__}:
-        __output_fields__
+        ||output|fields||
 
         """,
         0,
-    ).replace("__output_fields__", output_fields)
+    ).replace("||output|fields||", output_fields)
 
 
 class NextflowProcessPreAdapterTask(NextflowBaseTask):
@@ -105,11 +105,11 @@ class NextflowProcessPreAdapterTask(NextflowBaseTask):
             rf"""
                 @task(cache=True)
                 def {self.name}(
-                __params__
+                ||params||
                 ) -> Res_{self.id}:
                 """,
             0,
-        ).replace("__params__", params_str)
+        ).replace("||params||", params_str)
 
         return res
 
@@ -198,11 +198,11 @@ class NextflowProcessPostAdapterTask(NextflowBaseTask):
         res += reindent(
             rf"""
             class Res{self.name}(NamedTuple):
-            __output_fields__
+            ||output|fields||
 
             """,
             0,
-        ).replace("__output_fields__", output_fields)
+        ).replace("||output|fields||", output_fields)
 
         res += get_dataclass_code(self.dataclass)
 
@@ -219,25 +219,12 @@ class NextflowProcessPostAdapterTask(NextflowBaseTask):
         return res
 
     def get_fn_return_stmt(self):
-        results: List[str] = []
-        for out_name in self._python_outputs.keys():
-            results.append(
-                reindent(
-                    rf"""
-                    {out_name}=json.dumps([*chain.from_iterable([json.loads(x.{out_name}) for x in default])])
-                    """,
-                    1,
-                ).rstrip()
-            )
-
-        return_str = ",\n".join(results)
-
         return reindent(
             rf"""
             return get_mapper_outputs(Res{self.name}, default)
             """,
             1,
-        ).replace("__return_str__", return_str)
+        )
 
     def get_fn_code(self, nf_script_path_in_container: Path):
         code_block = self.get_fn_interface()

{latch-2.39.0.dev33 → latch-2.39.0.dev35}/latch_cli/extras/nextflow/tasks/merge.py

@@ -74,11 +74,11 @@ class NextflowMergeTask(NextflowOperatorTask):
         return reindent(
             rf"""
                 return Res{self.name}(
-            __return_str__
+            ||return|str||
                 )
             """,
             0,
-        ).replace("__return_str__", return_str)
+        ).replace("||return|str||", return_str)
 
     def get_fn_code(self, nf_script_path_in_container: Path):
         code_block = self.get_fn_interface()

{latch-2.39.0.dev33 → latch-2.39.0.dev35}/latch_cli/extras/nextflow/tasks/operator.py

@@ -50,11 +50,11 @@ class NextflowOperatorTask(NextflowBaseTask):
             res += reindent(
                 rf"""
                 class Res{self.name}(NamedTuple):
-                __output_fields__
+                ||output|fields||
 
                 """,
                 0,
-            ).replace("__output_fields__", output_fields)
+            ).replace("||output|fields||", output_fields)
 
             outputs_str = f"Res{self.name}:"
 
@@ -73,13 +73,13 @@ class NextflowOperatorTask(NextflowBaseTask):
                 rf"""
                 @task(cache=True)
                 def {self.name}(
-                __params__
-                ) -> __outputs__
+                ||params||
+                ) -> ||outputs||
                 """,
                 0,
             )
-            .replace("__params__", params_str)
-            .replace("__outputs__", outputs_str)
+            .replace("||params||", params_str)
+            .replace("||outputs||", outputs_str)
         )
 
         return res
@@ -101,11 +101,11 @@ class NextflowOperatorTask(NextflowBaseTask):
         return reindent(
             rf"""
                     return Res{self.name}(
-                __return_str__
+                ||return|str||
                     )
             """,
             0,
-        ).replace("__return_str__", return_str)
+        ).replace("||return|str||", return_str)
 
     def get_fn_code(self, nf_script_path_in_container: Path):
         code_block = self.get_fn_interface()
@@ -188,17 +188,22 @@ class NextflowOperatorTask(NextflowBaseTask):
 
                     {download_str}
 
-                    subprocess.run(
-                        [{', '.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),
-                        }},
-                        check=True,
-                    )
+                    try:
+                        subprocess.run(
+                            [{', '.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),
+                            }},
+                            check=True,
+                        )
+                    except subprocess.CalledProcessError:
+                        log = Path("/root/.nextflow.log").read_text()
+                        print("\n\n\n\n\n" + log)
+                        raise
 
                     out_channels = {{}}
                     files = [Path(f) for f in glob.glob(".latch/task-outputs/*.json")]
@@ -214,12 +219,12 @@ class NextflowOperatorTask(NextflowBaseTask):
                         _override_task_status(status="SKIPPED")
                     except Exception as e:
                         print(f"Failed to override task status: {{e}}")
-                    out_channels = {{__skip__}}
+                    out_channels = {{||skip||}}
 
             """,
             1,
         ).replace(
-            "__skip__",
+            "||skip||",
             ", ".join([f"{repr(o)}: None" for o in self._python_outputs.keys()]),
         )
 

{latch-2.39.0.dev33 → latch-2.39.0.dev35}/latch_cli/extras/nextflow/tasks/process.py

@@ -96,11 +96,11 @@ class NextflowProcessTask(NextflowBaseTask):
         return reindent(
             rf"""
                     return {res_type.__name__}(
-                __return_str__
+                ||return|str||
                     )
             """,
             0,
-        ).replace("__return_str__", return_str)
+        ).replace("||return|str||", return_str)
 
     def get_fn_code(self, nf_script_path_in_container: Path):
         code_block = self.get_fn_interface()

{latch-2.39.0.dev33 → latch-2.39.0.dev35}/setup.py

@@ -13,17 +13,13 @@ if cur_ver < (3, 8) or cur_ver > (3, 11):
 
 setup(
     name="latch",
-    version="v2.39.0.dev33",
+    version="v2.39.0.dev35",
     author_email="kenny@latch.bio",
     description="The Latch SDK",
     packages=find_packages(),
     include_package_data=True,
     python_requires=">=3.8,<3.12",
-    entry_points={
-        "console_scripts": [
-            "latch=latch_cli.main:main",
-        ]
-    },
+    entry_points={"console_scripts": ["latch=latch_cli.main:main"]},
     install_requires=[
         "kubernetes>=24.2.0",
         "pyjwt>=0.2.0",