latch 2.39.0.dev22__tar.gz → 2.39.0.dev23__tar.gz

{latch-2.39.0.dev22/latch.egg-info → latch-2.39.0.dev23}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: latch
-Version: 2.39.0.dev22
+Version: 2.39.0.dev23
 Summary: The Latch SDK
 Author-email: kenny@latch.bio
 Classifier: Programming Language :: Python :: 3.8

{latch-2.39.0.dev22 → latch-2.39.0.dev23/latch.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: latch
-Version: 2.39.0.dev22
+Version: 2.39.0.dev23
 Summary: The Latch SDK
 Author-email: kenny@latch.bio
 Classifier: Programming Language :: Python :: 3.8

{latch-2.39.0.dev22 → latch-2.39.0.dev23}/latch.egg-info/SOURCES.txt

@@ -133,7 +133,13 @@ latch_cli/services/execute/utils.py
 latch_cli/services/init/__init__.py
 latch_cli/services/init/init.py
 latch_cli/services/init/__pycache__/__init__.cpython-310.pyc
+latch_cli/services/init/__pycache__/__init__.cpython-311.pyc
+latch_cli/services/init/__pycache__/__init__.cpython-38.pyc
+latch_cli/services/init/__pycache__/__init__.cpython-39.pyc
 latch_cli/services/init/__pycache__/init.cpython-310.pyc
+latch_cli/services/init/__pycache__/init.cpython-311.pyc
+latch_cli/services/init/__pycache__/init.cpython-38.pyc
+latch_cli/services/init/__pycache__/init.cpython-39.pyc
 latch_cli/services/init/assemble_and_sort/.env
 latch_cli/services/init/assemble_and_sort/LICENSE
 latch_cli/services/init/assemble_and_sort/README.md
@@ -141,22 +147,26 @@ latch_cli/services/init/assemble_and_sort/__init__.py
 latch_cli/services/init/assemble_and_sort/assemble.py
 latch_cli/services/init/assemble_and_sort/sort.py
 latch_cli/services/init/assemble_and_sort/system-requirements.txt
+latch_cli/services/init/assemble_and_sort/__pycache__/__init__.cpython-310.pyc
 latch_cli/services/init/common/.dockerignore
 latch_cli/services/init/example_conda/__init__.py
 latch_cli/services/init/example_conda/conda_task.py
 latch_cli/services/init/example_conda/environment.yaml
+latch_cli/services/init/example_conda/__pycache__/__init__.cpython-310.pyc
 latch_cli/services/init/example_docker/__init__.py
 latch_cli/services/init/example_docker/task.py
 latch_cli/services/init/example_nf_integration/Dockerfile
 latch_cli/services/init/example_nf_integration/main.nf
 latch_cli/services/init/example_nf_integration/workflow.nf
 latch_cli/services/init/example_nf_integration/latch_metadata/__init__.py
+latch_cli/services/init/example_nf_integration/latch_metadata/__pycache__/__init__.cpython-311.pyc
 latch_cli/services/init/example_nfcore/Dockerfile
 latch_cli/services/init/example_nfcore/__init__.py
 latch_cli/services/init/example_nfcore/task.py
 latch_cli/services/init/example_r/__init__.py
 latch_cli/services/init/example_r/environment.R
 latch_cli/services/init/example_r/r_task.py
+latch_cli/services/init/example_r/__pycache__/__init__.cpython-310.pyc
 latch_cli/services/init/example_snakemake/Dockerfile
 latch_cli/services/init/example_snakemake/Snakefile
 latch_cli/services/init/example_snakemake/config.yaml
@@ -169,6 +179,7 @@ latch_cli/services/init/template/LICENSE
 latch_cli/services/init/template/README.md
 latch_cli/services/init/template/__init__.py
 latch_cli/services/init/template/task.py
+latch_cli/services/init/template/__pycache__/__init__.cpython-310.pyc
 latch_cli/services/register/__init__.py
 latch_cli/services/register/constants.py
 latch_cli/services/register/register.py

{latch-2.39.0.dev22 → latch-2.39.0.dev23}/latch_cli/extras/nextflow/build.py

@@ -3,7 +3,7 @@ import os
 import shutil
 import subprocess
 import sys
-from collections import OrderedDict
+from collections import OrderedDict, defaultdict
 from pathlib import Path
 from textwrap import dedent
 from typing import Dict, List, Optional, cast
@@ -86,6 +86,7 @@ def build_from_nextflow_dag(
 
         task_bindings: List[literals_models.Binding] = [*global_wf_input_bindings]
         branches: Dict[str, bool] = {}
+        merge_sources: Dict[str, List[str]] = defaultdict(lambda: [])
         for dep, edge in wf.dag.ancestors()[vertex]:
             if dep.type == VertexType.Conditional:
                 input_name = f"condition_{dep.id}"
@@ -98,11 +99,15 @@ def build_from_nextflow_dag(
                 node = NodeOutput(node=node_map[dep.id], var=f"condition")
             else:
                 input_name = f"channel_{dep.id}"
-                output_name = "res"
 
+                output_name = "res"
                 if len(dep.outputNames) > 0:
                     idx = int(edge.label)
-                    input_name = output_name = dep.outputNames[idx]
+                    input_name = f"{input_name}_{idx}"
+                    output_name = dep.outputNames[idx]
+
+                if vertex.type == VertexType.Merge:
+                    merge_sources[output_name].append(input_name)
 
                 task_inputs[input_name] = Optional[str]
 
@@ -123,6 +128,8 @@ def build_from_nextflow_dag(
             upstream_nodes.append(node_map[dep.id])
 
         node_name = get_node_name(vertex.id)
+        if vertex.type == VertexType.Merge:
+            task_outputs = {k: Optional[str] for k in merge_sources.keys()}
 
         if vertex.type == VertexType.Process:
             pre_adapter_task = NextflowProcessPreAdapterTask(
@@ -265,6 +272,7 @@ def build_from_nextflow_dag(
                 name=vertex.label,
                 id=vertex.id,
                 branches=branches,
+                sources=merge_sources,
                 wf=wf,
             )
 

{latch-2.39.0.dev22 → latch-2.39.0.dev23}/latch_cli/extras/nextflow/tasks/conditional.py

@@ -33,7 +33,6 @@ class NextflowConditionalTask(NextflowOperatorTask):
         self.nf_task_type = NFTaskType.Conditional
 
     def get_fn_return_stmt(self):
-
         return reindent(
             rf"""
             res = out_channels.get("condition")

{latch-2.39.0.dev22 → latch-2.39.0.dev23}/latch_cli/extras/nextflow/tasks/merge.py

@@ -17,6 +17,7 @@ class NextflowMergeTask(NextflowOperatorTask):
         id: str,
         name: str,
         branches: Dict[str, bool],
+        sources: Dict[str, List[str]],
         wf: NextflowWorkflow,
     ):
         super().__init__(
@@ -30,6 +31,7 @@ class NextflowMergeTask(NextflowOperatorTask):
             wf,
         )
 
+        self.sources = sources
         self.nf_task_type = NFTaskType.Merge
 
     def get_fn_conditions(self):
@@ -59,7 +61,9 @@ class NextflowMergeTask(NextflowOperatorTask):
     def get_fn_return_stmt(self):
         results: List[str] = []
         for out_name in self._python_outputs.keys():
-            results.append(reindent(rf"{out_name}=res", 2).rstrip())
+            results.append(
+                reindent(rf"{out_name}=res.get({repr(out_name)})", 2).rstrip()
+            )
 
         return_str = ",\n".join(results)
 
@@ -76,18 +80,24 @@ class NextflowMergeTask(NextflowOperatorTask):
         code_block = self.get_fn_interface()
         code_block += self.get_fn_conditions()
 
-        expr = " or ".join(channel_input for channel_input in self.channel_inputs)
+        exprs = []
+        for out_name, inputs in self.sources.items():
+            expr = " or ".join(input for input in inputs)
+
+            exprs.append(f"{repr(out_name)}: {expr}")
+
+        expr = ", ".join(x for x in exprs)
 
         code_block += reindent(
             rf"""
-                res = {expr}
+                res = {{ {expr} }}
             else:
                 print("TASK SKIPPED")
                 try:
                     _override_task_status(status="SKIPPED")
                 except Exception as e:
                     print(f"Failed to override task status: {{e}}")
-                res = None
+                res = {{}}
 
             """,
             1,

{latch-2.39.0.dev22 → latch-2.39.0.dev23}/latch_cli/extras/snakemake/serialize.py

@@ -415,14 +415,14 @@ def generate_jit_register_code(
             print_and_write_build_logs,
             print_upload_logs,
         )
-        from latch_cli.snakemake.serialize import (
+        from latch_cli.extras.snakemake.serialize import (
             extract_snakemake_workflow,
             generate_snakemake_entrypoint,
             serialize_snakemake,
         )
         from latch_cli.utils import get_parameter_json_value, check_exists_and_rename
-        import latch_cli.snakemake
-        from latch_cli.snakemake.serialize_utils import update_mapping
+        import latch_cli.extras.snakemake
+        from latch_cli.extras.snakemake.serialize_utils import update_mapping
         from latch_cli.utils import urljoins
 
         from latch import small_task

{latch-2.39.0.dev22 → latch-2.39.0.dev23}/setup.py

@@ -13,7 +13,7 @@ if cur_ver < (3, 8) or cur_ver > (3, 11):
 
 setup(
     name="latch",
-    version="v2.39.0.dev22",
+    version="v2.39.0.dev23",
     author_email="kenny@latch.bio",
     description="The Latch SDK",
     packages=find_packages(),