latch 2.40.4.dev2__tar.gz → 2.40.4.dev4__tar.gz

latch-2.40.4.dev4/PKG-INFO

@@ -0,0 +1,13 @@
+Metadata-Version: 2.1
+Name: latch
+Version: 2.40.4.dev4
+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-2.40.4.dev2 → latch-2.40.4.dev4}/latch/types/metadata.py

@@ -4,7 +4,9 @@ from enum import Enum
 from pathlib import Path
 from textwrap import indent
 from typing import (
+    Annotated,
     Any,
+    Callable,
     ClassVar,
     Collection,
     Dict,
@@ -478,6 +480,10 @@ class NextflowParameter(Generic[T], LatchParameter):
     """
     default: Optional[T] = None
 
+    def __post_init__(self):
+        if self.samplesheet is True:
+            self.type = Annotated[self.type, "samplesheet"]
+
 
 @dataclass
 class NextflowFileParameter(NextflowParameter[Union[LatchFile, LatchDir]]):
@@ -547,6 +553,10 @@ class LatchMetadata:
     """ A `LatchAuthor` object that describes the author of the workflow"""
     documentation: Optional[str] = None
     """A link to documentation for the workflow itself"""
+    about_page_markdown: Optional[Path] = None
+    """A path to a markdown file that will be rendered as the workflow About
+    page. If provided, it will override the docstring markdown, if it exists,
+    for SDK workflows."""
     repository: Optional[str] = None
     """A link to the repository where the code for the workflow is hosted"""
     license: str = "MIT"
@@ -571,6 +581,8 @@ class LatchMetadata:
         metadata_dict = asdict(self)
         # remove parameters since that will be handled by each parameters' dict() method
         del metadata_dict["parameters"]
+        # pyyaml is unable to serialize PosixPath objects + unused after registration
+        del metadata_dict["about_page_markdown"]
         metadata_dict["license"] = {"id": self.license}
 
         # flows override all other rendering, so disable them entirely if not provided

latch-2.40.4.dev4/latch.egg-info/PKG-INFO

@@ -0,0 +1,13 @@
+Metadata-Version: 2.1
+Name: latch
+Version: 2.40.4.dev4
+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-2.40.4.dev2 → latch-2.40.4.dev4}/latch.egg-info/SOURCES.txt

@@ -136,13 +136,7 @@ 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
@@ -150,25 +144,24 @@ 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.swn
+latch_cli/services/init/example_docker/.__init__.py.swo
+latch_cli/services/init/example_docker/.__init__.py.swp
 latch_cli/services/init/example_docker/__init__.py
 latch_cli/services/init/example_docker/task.py
 latch_cli/services/init/example_nextflow/main.nf
 latch_cli/services/init/example_nextflow/nextflow.config
 latch_cli/services/init/example_nextflow/workflow.nf
-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
@@ -181,7 +174,6 @@ 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-2.40.4.dev2 → latch-2.40.4.dev4}/latch.egg-info/requires.txt

@@ -7,7 +7,7 @@ paramiko>=3.2.0
 scp>=0.14.0
 boto3>=1.26.0
 tqdm>=4.63.0
-lytekit==0.15.5
+lytekit==0.15.6
 lytekitplugins-pods==0.6.2
 typing-extensions==4.7.1
 apscheduler==3.9.1

{latch-2.40.4.dev2 → latch-2.40.4.dev4}/latch_cli/extras/common/utils.py

@@ -37,13 +37,23 @@ def is_blob_type(typ: Type) -> TypeGuard[Union[Type[LatchFile], Type[LatchDir]]]
 
 
 def is_downloadable_blob_type(typ: Type):
-    if not is_blob_type(typ):
+    if not is_blob_type(typ) or typ is LatchOutputDir:
         return False
 
-    return typ is not LatchOutputDir
+    origin = get_origin(typ)
+    if origin is not None:
+        return all([
+            is_downloadable_blob_type(sub_typ) or sub_typ is type(None)
+            for sub_typ in get_args(typ)
+        ])
+
+    return True
 
 
 def type_repr(t: Type, *, add_namespace: bool = False) -> str:
+    if get_origin(t) == Annotated:
+        return type_repr(get_args(t)[0])
+
     if getattr(t, "__name__", None) == "NoneType":
         return "None"
 
@@ -70,3 +80,7 @@ def type_repr(t: Type, *, add_namespace: bool = False) -> str:
         )
 
     return getattr(t, "__name__", repr(t))
+
+
+def is_samplesheet_param(t: Type) -> bool:
+    return get_origin(t) == Annotated and get_args(t)[-1] == "samplesheet"

{latch-2.40.4.dev2 → latch-2.40.4.dev4}/latch_cli/extras/nextflow/build.py

@@ -31,7 +31,7 @@ from ...click_utils import italic
 from ...menus import select_tui
 from ...utils import current_workspace, identifier_from_str
 from ..common.serialize import binding_from_python
-from ..common.utils import reindent
+from ..common.utils import is_samplesheet_param, reindent
 from .dag import DAG, VertexType
 from .tasks.adapters import (
     NextflowProcessPostAdapterTask,
@@ -523,6 +523,14 @@ def generate_nf_entrypoint(
         0,
     )
 
+    if any([is_samplesheet_param(t) for t in wf.python_interface.inputs.values()]):
+        preamble += reindent(
+            r"""
+            from latch_metadata.parameters import  construct_samplesheet
+            """,
+            0,
+        )
+
     for t in wf.python_interface.inputs.values():
         preamble += get_preamble(t, make_optionals=True)
 

{latch-2.40.4.dev2 → latch-2.40.4.dev4}/latch_cli/extras/nextflow/tasks/operator.py

@@ -1,12 +1,12 @@
 import json
 from pathlib import Path
-from typing import Dict, List, Mapping, Type
+from typing import Annotated, Dict, List, Mapping, Type, get_args, get_origin
 
 from latch.types.directory import LatchDir
 from latch.types.file import LatchFile
 from latch.types.metadata import ParameterType
 
-from ...common.utils import is_blob_type, reindent, type_repr
+from ...common.utils import is_blob_type, is_samplesheet_param, reindent, type_repr
 from ..workflow import NextflowWorkflow
 from .base import NextflowBaseTask, NFTaskType
 
@@ -151,6 +151,13 @@ class NextflowOperatorTask(NextflowBaseTask):
                     """,
                     2,
                 )
+            elif is_samplesheet_param(typ):
+                code_block += reindent(
+                    f"""
+                    {k} = construct_samplesheet({k})
+                    """,
+                    2,
+                )
 
         # todo(ayush): figure out how to make this work
         do_file_io = False

{latch-2.40.4.dev2 → latch-2.40.4.dev4}/latch_cli/extras/nextflow/tasks/process.py

@@ -1,13 +1,18 @@
 import json
 from dataclasses import fields, is_dataclass
 from pathlib import Path
-from typing import List, Mapping, Optional, Type
+from typing import Annotated, List, Mapping, Optional, Type
+
+try:
+    from typing import get_args, get_origin
+except ImportError:
+    from typing_extensions import get_args, get_origin
 
 from latch.types.directory import LatchDir
 from latch.types.file import LatchFile
 from latch.types.metadata import ParameterType
 
-from ...common.utils import is_blob_type, reindent, type_repr
+from ...common.utils import is_blob_type, is_samplesheet_param, reindent, type_repr
 from ..workflow import NextflowWorkflow
 from .base import NextflowBaseTask, NFTaskType
 
@@ -165,6 +170,13 @@ class NextflowProcessTask(NextflowBaseTask):
                     """,
                     1,
                 )
+            elif is_samplesheet_param(typ):
+                code_block += reindent(
+                    f"""
+                    {k} = construct_samplesheet({k})
+                    """,
+                    1,
+                )
 
         if self.script_path.resolve() != self.wf.nf_script.resolve():
             stem = self.script_path.resolve().relative_to(self.wf.pkg_root.resolve())

{latch-2.40.4.dev2 → latch-2.40.4.dev4}/latch_cli/extras/nextflow/workflow.py

@@ -2,6 +2,7 @@ from dataclasses import fields, is_dataclass
 from pathlib import Path
 from typing import Any, Dict, List, Tuple, Type
 
+import click
 from flytekit.core.class_based_resolver import ClassStorageTaskResolver
 from flytekit.core.docstring import Docstring
 from flytekit.core.interface import Interface
@@ -48,9 +49,19 @@ class NextflowWorkflow(WorkflowBase, ClassStorageTaskResolver):
 
         self.output_directory = metadata._nextflow_metadata.output_directory
         self.docker_metadata = metadata._nextflow_metadata.docker_metadata
-
+        md_path = metadata._nextflow_metadata.about_page_markdown
+
+        if md_path is not None and md_path.exists():
+            click.secho(f"Rendering workflow About page content from {md_path}")
+            markdown_content = md_path.read_text()
+        else:
+            markdown_content = (
+                "Add markdown content to a file and add the path",
+                "to your workflow metadata to populate this page.\nMore information",
+                "[here](https://wiki.latch.bio/docs/nextflow/quickstart).",
+            )
         docstring = Docstring(
-            f"{metadata._nextflow_metadata.display_name}\n\nSample Description\n\n"
+            f"{metadata._nextflow_metadata.display_name}\n\n{markdown_content}\n\n"
             + str(metadata._nextflow_metadata)
         )
         python_interface = Interface(

{latch-2.40.4.dev2 → latch-2.40.4.dev4}/latch_cli/main.py

@@ -81,8 +81,6 @@ def main():
             fg="yellow",
         )
 
-    # crash_handler.init()
-
 
 """
 LOGIN COMMANDS

{latch-2.40.4.dev2 → latch-2.40.4.dev4}/latch_cli/services/register/utils.py

@@ -102,7 +102,6 @@ def build_image(
         tag=f"{ctx.dkr_repo}/{image_name}",
         decode=True,
     )
-
     return build_logs
 
 

{latch-2.40.4.dev2 → latch-2.40.4.dev4}/setup.py

@@ -13,7 +13,7 @@ if cur_ver < (3, 8) or cur_ver > (3, 11):
 
 setup(
     name="latch",
-    version="v2.40.4.dev2",
+    version="v2.40.4.dev4",
     author_email="kenny@latch.bio",
     description="The Latch SDK",
     packages=find_packages(),
@@ -30,7 +30,7 @@ setup(
         "scp>=0.14.0",
         "boto3>=1.26.0",
         "tqdm>=4.63.0",
-        "lytekit==0.15.5",
+        "lytekit==0.15.6",
         "lytekitplugins-pods==0.6.2",
         "typing-extensions==4.7.1",
         "apscheduler==3.9.1",

latch-2.40.4.dev2/PKG-INFO

@@ -1,39 +0,0 @@
-Metadata-Version: 2.1
-Name: latch
-Version: 2.40.4.dev2
-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==0.15.5
-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-2.40.4.dev2/latch.egg-info/PKG-INFO

@@ -1,39 +0,0 @@
-Metadata-Version: 2.1
-Name: latch
-Version: 2.40.4.dev2
-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==0.15.5
-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"