latch 2.39.0.dev12__tar.gz → 2.39.0.dev14__tar.gz

latch-2.39.0.dev14/PKG-INFO

@@ -0,0 +1,39 @@
+Metadata-Version: 2.1
+Name: latch
+Version: 2.39.0.dev14
+Summary: The Latch SDK
+Author-email: kenny@latch.bio
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Requires-Python: >=3.8,<3.12
+License-File: LICENSE
+Requires-Dist: kubernetes>=24.2.0
+Requires-Dist: pyjwt>=0.2.0
+Requires-Dist: requests>=2.28.1
+Requires-Dist: click>=8.0
+Requires-Dist: docker>=5.0
+Requires-Dist: paramiko>=3.2.0
+Requires-Dist: scp>=0.14.0
+Requires-Dist: boto3>=1.26.0
+Requires-Dist: tqdm>=4.63.0
+Requires-Dist: lytekit==0.15.3
+Requires-Dist: lytekitplugins-pods==0.6.2
+Requires-Dist: typing-extensions==4.7.1
+Requires-Dist: apscheduler==3.9.1
+Requires-Dist: gql==3.4.0
+Requires-Dist: graphql-core==3.2.3
+Requires-Dist: requests-toolbelt==0.10.1
+Requires-Dist: latch-sdk-gql==0.0.6
+Requires-Dist: latch-sdk-config==0.0.4
+Requires-Dist: python-dateutil>=2.8
+Requires-Dist: aioconsole==0.6.1
+Requires-Dist: asyncssh==2.13.2
+Requires-Dist: websockets==11.0.3
+Requires-Dist: watchfiles==0.19.0
+Provides-Extra: snakemake
+Requires-Dist: snakemake<7.30.2,>=7.18.0; extra == "snakemake"
+Requires-Dist: pulp<2.8,>=2.0; extra == "snakemake"
+Provides-Extra: pandas
+Requires-Dist: pandas>=2.0.0; extra == "pandas"

latch-2.39.0.dev14/latch.egg-info/PKG-INFO

@@ -0,0 +1,39 @@
+Metadata-Version: 2.1
+Name: latch
+Version: 2.39.0.dev14
+Summary: The Latch SDK
+Author-email: kenny@latch.bio
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Requires-Python: >=3.8,<3.12
+License-File: LICENSE
+Requires-Dist: kubernetes>=24.2.0
+Requires-Dist: pyjwt>=0.2.0
+Requires-Dist: requests>=2.28.1
+Requires-Dist: click>=8.0
+Requires-Dist: docker>=5.0
+Requires-Dist: paramiko>=3.2.0
+Requires-Dist: scp>=0.14.0
+Requires-Dist: boto3>=1.26.0
+Requires-Dist: tqdm>=4.63.0
+Requires-Dist: lytekit==0.15.3
+Requires-Dist: lytekitplugins-pods==0.6.2
+Requires-Dist: typing-extensions==4.7.1
+Requires-Dist: apscheduler==3.9.1
+Requires-Dist: gql==3.4.0
+Requires-Dist: graphql-core==3.2.3
+Requires-Dist: requests-toolbelt==0.10.1
+Requires-Dist: latch-sdk-gql==0.0.6
+Requires-Dist: latch-sdk-config==0.0.4
+Requires-Dist: python-dateutil>=2.8
+Requires-Dist: aioconsole==0.6.1
+Requires-Dist: asyncssh==2.13.2
+Requires-Dist: websockets==11.0.3
+Requires-Dist: watchfiles==0.19.0
+Provides-Extra: snakemake
+Requires-Dist: snakemake<7.30.2,>=7.18.0; extra == "snakemake"
+Requires-Dist: pulp<2.8,>=2.0; extra == "snakemake"
+Provides-Extra: pandas
+Requires-Dist: pandas>=2.0.0; extra == "pandas"

{latch-2.39.0.dev12 → latch-2.39.0.dev14}/latch.egg-info/SOURCES.txt

@@ -84,6 +84,7 @@ latch_cli/extras/common/serialize.py
 latch_cli/extras/common/utils.py
 latch_cli/extras/nextflow/__init__.py
 latch_cli/extras/nextflow/build.py
+latch_cli/extras/nextflow/channel.py
 latch_cli/extras/nextflow/dag.py
 latch_cli/extras/nextflow/file_persistence.py
 latch_cli/extras/nextflow/serialize.py

{latch-2.39.0.dev12 → latch-2.39.0.dev14}/latch_cli/extras/nextflow/build.py

@@ -410,7 +410,7 @@ def build_nf_wf(
     }
 
     if os.environ.get("LATCH_NEXTFLOW_DEV") is not None:
-        env = {**os.environ}
+        env = os.environ
 
     try:
         subprocess.run(
@@ -501,6 +501,7 @@ def generate_nf_entrypoint(
 
         from flytekit.extras.persistence import LatchPersistence
         from latch_cli.extras.nextflow.file_persistence import download_files, stage_for_output, upload_files
+        from latch_cli.extras.nextflow.channel import get_mapper_inputs
         from latch_cli.utils import check_exists_and_rename, get_parameter_json_value, urljoins
 
         from latch.resources.tasks import custom_task

latch-2.39.0.dev14/latch_cli/extras/nextflow/channel.py

@@ -0,0 +1,39 @@
+import json
+from typing import Dict, List, Type, TypeVar
+
+from latch.types.metadata import _IsDataclass
+
+T = TypeVar("T", bound=_IsDataclass)
+
+
+def get_mapper_inputs(
+    cls: Type[T],
+    wf_inputs: Dict[str, object],
+    channel_inputs: Dict[str, str],
+) -> List[T]:
+    value_channels = {}
+    queue_channels = {}
+
+    min_len = float("inf")
+    for param_name, channel in channel_inputs.items():
+        values = json.loads(channel)
+
+        if type(values) == list:
+            queue_channels[param_name] = values
+            min_len = min(min_len, len(values))
+        else:
+            value_channels[param_name] = values
+
+    if min_len == float("inf"):
+        min_len = 1
+
+    res: List[T] = []
+    for i in range(min_len):
+        kwargs = {**wf_inputs, **value_channels}
+
+        for k, v in queue_channels.items():
+            kwargs[k] = v[i]
+
+        res.append(cls(**kwargs))
+
+    return res

{latch-2.39.0.dev12 → latch-2.39.0.dev14}/latch_cli/extras/nextflow/tasks/adapters.py

@@ -1,5 +1,5 @@
 import typing
-from dataclasses import dataclass, fields, make_dataclass
+from dataclasses import Field, dataclass, fields, make_dataclass
 from pathlib import Path
 from typing import Dict, List, Mapping, Type, Union, get_args, get_origin
 
@@ -116,36 +116,27 @@ class NextflowProcessPreAdapterTask(NextflowBaseTask):
 
         fs = fields(self.dataclass)
 
-        channel_fields = [f for f in fs if not f.name.startswith("wf_")]
-        if len(channel_fields) == 0:
-            field_str = ", ".join(f"{f.name}={f.name}" for f in fs)
-
-            code_block += reindent(
-                f"""
-                result = [Dataclass_{self.id}(__fields__)]
-                """.replace("__fields__", field_str),
-                2,
-            )
-        else:
-            assignment_str = ", ".join(
-                [f"{field.name}=x[{i}]" for i, field in enumerate(fs)]
-            )
+        channel_fields: List[Field] = []
+        wf_fields: List[Field] = []
+        for f in fs:
+            if f.name.startswith("wf_"):
+                wf_fields.append(f)
+            else:
+                channel_fields.append(f)
 
-            variables = ", ".join([
-                (
-                    f"repeat({field.name})"
-                    if field.name.startswith("wf_")
-                    else f"map(lambda x: json.dumps([x]), json.loads({field.name}))"
-                )
-                for field in fs
-            ])
+        wf_dict_str = (
+            "{" + ", ".join(f"{repr(f.name)}: {f.name}" for f in wf_fields) + "}"
+        )
+        channel_dict_str = (
+            "{" + ", ".join(f"{repr(f.name)}: {f.name}" for f in channel_fields) + "}"
+        )
 
-            code_block += reindent(
-                rf"""
-                result = [Dataclass_{self.id}({assignment_str}) for x in zip({variables})]
-                """,
-                2,
-            )
+        code_block += reindent(
+            f"""
+            result = get_mapper_inputs({self.dataclass.__name__}, {wf_dict_str}, {channel_dict_str})
+            """,
+            2,
+        )
 
         code_block += reindent(
             rf"""

{latch-2.39.0.dev12 → latch-2.39.0.dev14}/latch_cli/extras/nextflow/tasks/operator.py

@@ -160,6 +160,7 @@ class NextflowOperatorTask(NextflowBaseTask):
             "splitFastq",
             "splitJson",
             "splitText",
+            "fromPath",
         ]:
             if op_name in self.name:
                 do_file_io = True

{latch-2.39.0.dev12 → latch-2.39.0.dev14}/setup.py

@@ -13,7 +13,7 @@ if cur_ver < (3, 8) or cur_ver > (3, 11):
 
 setup(
     name="latch",
-    version="v2.39.0.dev12",
+    version="v2.39.0.dev14",
     author_email="kenny@latch.bio",
     description="The Latch SDK",
     packages=find_packages(),

latch-2.39.0.dev12/PKG-INFO

@@ -1,13 +0,0 @@
-Metadata-Version: 2.1
-Name: latch
-Version: 2.39.0.dev12
-Summary: The Latch SDK
-Author-email: kenny@latch.bio
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Requires-Python: >=3.8,<3.12
-Provides-Extra: snakemake
-Provides-Extra: pandas
-License-File: LICENSE

latch-2.39.0.dev12/latch.egg-info/PKG-INFO

@@ -1,13 +0,0 @@
-Metadata-Version: 2.1
-Name: latch
-Version: 2.39.0.dev12
-Summary: The Latch SDK
-Author-email: kenny@latch.bio
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Requires-Python: >=3.8,<3.12
-Provides-Extra: snakemake
-Provides-Extra: pandas
-License-File: LICENSE