latch 2.39.0.dev2__tar.gz → 2.39.0.dev4__tar.gz

{latch-2.39.0.dev2/latch.egg-info → latch-2.39.0.dev4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: latch
-Version: 2.39.0.dev2
+Version: 2.39.0.dev4
 Summary: The Latch SDK
 Author-email: kenny@latch.bio
 Classifier: Programming Language :: Python :: 3.8

{latch-2.39.0.dev2 → latch-2.39.0.dev4/latch.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: latch
-Version: 2.39.0.dev2
+Version: 2.39.0.dev4
 Summary: The Latch SDK
 Author-email: kenny@latch.bio
 Classifier: Programming Language :: Python :: 3.8

{latch-2.39.0.dev2 → latch-2.39.0.dev4}/latch_cli/extras/nextflow/build.py

@@ -386,6 +386,19 @@ def build_nf_wf(pkg_root: Path, nf_script: Path) -> NextflowWorkflow:
     for f in old_dag_files:
         f.unlink()
 
+    env = {
+        **os.environ,
+        # read NF binaries from `.latch/.nextflow` instead of system
+        "NXF_HOME": str(pkg_root / ".latch" / ".nextflow"),
+        # don't display version mismatch warning
+        "NXF_DISABLE_CHECK_LATEST": "true",
+        # don't emit .nextflow.log files
+        "NXF_LOG_FILE": "/dev/null",
+    }
+
+    if os.environ.get("LATCH_NEXTFLOW_DEV") is not None:
+        env = {**os.environ}
+
     try:
         subprocess.run(
             [
@@ -395,15 +408,7 @@ def build_nf_wf(pkg_root: Path, nf_script: Path) -> NextflowWorkflow:
                 str(nf_script.resolve()),
                 "-latchRegister",
             ],
-            env={
-                **os.environ,
-                # read NF binaries from `.latch/.nextflow` instead of system
-                "NXF_HOME": str(pkg_root / ".latch" / ".nextflow"),
-                # don't display version mismatch warning
-                "NXF_DISABLE_CHECK_LATEST": "true",
-                # don't emit .nextflow.log files
-                "NXF_LOG_FILE": "/dev/null",
-            },
+            env=env,
             check=True,
         )
     except subprocess.CalledProcessError as e:

{latch-2.39.0.dev2 → latch-2.39.0.dev4}/latch_cli/extras/nextflow/file_persistence.py

@@ -46,7 +46,7 @@ def _extract_paths(parameter: JSONValue, res: List[Path]):
     if k == "path":
         assert isinstance(v, str)
 
-        res.append(Path(v).resolve())
+        res.append(Path(v).absolute())
     elif k == "list":
         assert isinstance(v, List)
 
@@ -120,9 +120,9 @@ def download_files(channels: List[List[JSONValue]], outdir: LatchDir):
         local.parent.mkdir(parents=True, exist_ok=True)
 
         if data.type == LDataNodeType.obj:
-            lp.download(remote, local)
+            lp.download(remote, str(local))
         else:
-            lp.download_directory(remote, local)
+            lp.download_directory(remote, str(local))
 
         click.echo("Done.")
 
@@ -140,9 +140,9 @@ def _upload(local: Path, remote: str):
     click.echo(f"Uploading {local} -> {remote}. ", nl=False)
 
     if p.is_file():
-        lp.upload(local, remote)
+        lp.upload(str(local), remote)
     else:
-        lp.upload_directory(local, remote)
+        lp.upload_directory(str(local), remote)
 
     click.echo("Done.")
 

{latch-2.39.0.dev2 → latch-2.39.0.dev4}/latch_cli/extras/nextflow/serialize.py

@@ -8,4 +8,4 @@ def serialize_nf(
     image_name: str,
     dkr_repo: str,
 ):
-    serialize(nf_wf, output_dir, image_name, dkr_repo, write_spec=False)
+    serialize(nf_wf, output_dir, image_name, dkr_repo, write_spec=True)

{latch-2.39.0.dev2 → latch-2.39.0.dev4}/latch_cli/extras/nextflow/tasks/base.py

@@ -34,6 +34,9 @@ class NextflowBaseTask(PythonAutoContainerTask[Pod]):
         name: str,
         branches: Dict[str, bool],
         wf: NextflowWorkflow,
+        # todo(ayush): expose / infer these somehow
+        cpu: int = 4,
+        memory: int = 8,
     ):
         self.id = id
         self.wf = wf
@@ -56,16 +59,12 @@ class NextflowBaseTask(PythonAutoContainerTask[Pod]):
 
         self.branches = branches
 
-        # todo(ayush): expose / infer these somehow
-        cores = 4
-        mem = 7  # GiB
-
         super().__init__(
             task_type=SdkTaskType.SIDECAR_TASK,
             task_type_version=2,
             name=f"{name}_{id}",
             interface=interface,
-            task_config=custom_task(cpu=cores, memory=mem).keywords["task_config"],
+            task_config=custom_task(cpu=cpu, memory=memory).keywords["task_config"],
             task_resolver=NextflowBaseTaskResolver(),
         )
 

{latch-2.39.0.dev2 → latch-2.39.0.dev4}/latch_cli/extras/nextflow/tasks/operator.py

@@ -109,8 +109,6 @@ class NextflowOperatorTask(NextflowBaseTask):
             "/root/nextflow",
             "run",
             str(nf_script_path_in_container),
-            "-profile",
-            "mamba",
         ]
 
         for flag, val in self.wf.flags_to_params.items():

{latch-2.39.0.dev2 → latch-2.39.0.dev4}/latch_cli/extras/nextflow/tasks/process.py

@@ -24,7 +24,7 @@ class NextflowProcessTask(NextflowBaseTask):
         unaliased: str,
         wf: NextflowWorkflow,
     ):
-        super().__init__(inputs, outputs, id, name, {}, wf)
+        super().__init__(inputs, outputs, id, name, {}, wf, cpu=16, memory=32)
 
         self.wf_inputs = {}
         self.conditional_inputs = {}
@@ -101,8 +101,6 @@ class NextflowProcessTask(NextflowBaseTask):
             "/root/nextflow",
             "run",
             str(nf_script_path_in_container),
-            "-profile",
-            "mamba",
         ]
 
         for flag, val in self.wf.flags_to_params.items():

{latch-2.39.0.dev2 → latch-2.39.0.dev4}/setup.py

@@ -13,7 +13,7 @@ if cur_ver < (3, 8) or cur_ver > (3, 11):
 
 setup(
     name="latch",
-    version="v2.39.0.dev2",
+    version="v2.39.0.dev4",
     author_email="kenny@latch.bio",
     description="The Latch SDK",
     packages=find_packages(),