dur

Signed-off-by: Ayush Kamat <[email protected]>

Author: ayushkamat

src/latch_cli/constants.py

@@ -5,7 +5,7 @@
 
 class Units(int, Enum):
     KiB = 2**10
-    kB = 10**3
+    kB = 10**3  # noqa: N815
 
     MiB = 2**20
     MB = 10**6
@@ -22,7 +22,7 @@ class LatchConstants:
     base_image: str = (
         "812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base:cb01-main"
     )
-    nextflow_latest_version: str = "v2.3.0"
+    nextflow_latest_version: str = "v3.0.5"
 
     file_max_size: int = 4 * Units.MiB
     file_chunk_size: int = 64 * Units.MiB

src/latch_cli/docker_utils/__init__.py

@@ -425,11 +425,13 @@ def generate_dockerignore(
     click.secho(f"Successfully generated .dockerignore `{dest}`", fg="green")
 
 
-def get_default_dockerfile(pkg_root: Path, *, wf_type: WorkflowType, overwrite: bool = False):
+def get_default_dockerfile(
+    pkg_root: Path, *, wf_type: WorkflowType, overwrite: bool = False
+):
     default_dockerfile = pkg_root / "Dockerfile"
 
     config = get_or_create_workflow_config(
-        pkg_root=pkg_root,
+        pkg_root / ".latch" / "config",
         base_image_type=BaseImageOptions.nextflow
         if wf_type == WorkflowType.nextflow
         else BaseImageOptions.default,

src/latch_cli/main.py

@@ -239,6 +239,12 @@ def init(
     type=click.Path(exists=True, dir_okay=False, path_type=Path),
     help="Path to a direnv file (.env) containing environment variables to inject into the container.",
 )
+@click.option(
+    "--output",
+    "-o",
+    type=click.Path(exists=True, dir_okay=False, path_type=Path),
+    help="Where to write the result Dockerfile. Default is Dockerfile in the root of the workflow directory.",
+)
 def dockerfile(
     pkg_root: Path,
     snakemake: bool = False,
@@ -250,6 +256,7 @@ def dockerfile(
     pyproject: Optional[Path] = None,
     pip_requirements: Optional[Path] = None,
     direnv: Optional[Path] = None,
+    output: Optional[Path] = None,
 ):
     """Generates a user editable dockerfile for a workflow and saves under `pkg_root/Dockerfile`.
 
@@ -275,8 +282,11 @@ def dockerfile(
         workflow_type = WorkflowType.nextflow
         base_image = BaseImageOptions.nextflow
 
+    if output is None:
+        output = pkg_root / "Dockerfile"
+
     config = get_or_create_workflow_config(
-        pkg_root=pkg_root, base_image_type=base_image
+        output.parent / ".latch" / "config", base_image_type=base_image
     )
 
     builder = DockerfileBuilder(
@@ -290,7 +300,7 @@ def dockerfile(
         pip_requirements=pip_requirements,
         direnv=direnv,
     )
-    builder.generate(overwrite=force)
+    builder.generate(dest=output, overwrite=force)
 
     if not click.confirm("Generate a .dockerignore?"):
         return

src/latch_cli/nextflow/parse_schema.py

@@ -2,7 +2,7 @@
 from dataclasses import dataclass
 from pathlib import Path
 from textwrap import indent
-from typing import Generic, Literal, Optional, TypedDict, TypeVar, Union
+from typing import Literal, Optional, TypedDict, Union
 
 import click
 from typing_extensions import NotRequired, TypeAlias
@@ -63,17 +63,33 @@ class NfBooleanType(TypedDict):
     metadata: CommonMetadata
 
 
-EnumT = TypeVar("EnumT", str, int, float)
+class NfStringEnumType(TypedDict):
+    type: Literal["enum"]
+    flavor: Literal["string"]
+    values: list[str]
+    default: NotRequired[str]
+    metadata: CommonMetadata
+
+
+class NfIntegerEnumType(TypedDict):
+    type: Literal["enum"]
+    flavor: Literal["integer"]
+    values: list[int]
+    default: NotRequired[int]
+    metadata: CommonMetadata
 
 
-class NfEnumType(TypedDict, Generic[EnumT]):
+class NfNumberEnumType(TypedDict):
     type: Literal["enum"]
-    flavor: Literal["string", "integer", "number"]
-    values: list[EnumT]
-    default: NotRequired[EnumT]
+    flavor: Literal["number"]
+    values: list[float]
+    default: NotRequired[float]
     metadata: CommonMetadata
 
 
+NfEnumType: TypeAlias = Union[NfStringEnumType, NfIntegerEnumType, NfNumberEnumType]
+
+
 class NfArrayType(TypedDict):
     type: Literal["array"]
     default: NotRequired[list]
@@ -106,9 +122,7 @@ class NfBlobType(TypedDict):
     NfStringType,
     NfIntegerType,
     NfFloatType,
-    NfEnumType[str],
-    NfEnumType[float],
-    NfEnumType[int],
+    NfEnumType,
     NfBooleanType,
     NfArrayType,
     NfObjectType,
@@ -261,7 +275,7 @@ def parse_bool(
 
 def parse_enum(
     param_name: str, properties: dict[str, object], required_set: set[str]
-) -> Union[NfEnumType[str], NfEnumType[int], NfEnumType[float]]:
+) -> NfEnumType:
     typ = properties["type"]
     assert "enum" in properties
 
@@ -277,13 +291,37 @@ def parse_enum(
     assert values is not None, "enum parameter must specify a set of `values`"
     assert isinstance(values, list), "`values` must be a list"
 
-    # todo(ayush): fix type errors here
-    return NfEnumType(
+    if typ == "string":
+        assert default is None or isinstance(default, str), "default must be a string"
+
+        return NfStringEnumType(
+            type="enum",
+            flavor="string",
+            values=values,
+            metadata=metadata,
+            **({"default": default} if default is not None else {}),
+        )
+    if typ == "integer":
+        assert default is None or isinstance(default, int), "default must be an integer"
+
+        return NfIntegerEnumType(
+            type="enum",
+            flavor="integer",
+            values=values,
+            metadata=metadata,
+            **({"default": default} if default is not None else {}),
+        )
+
+    assert default is None or isinstance(default, (int, float)), (
+        "default must be a number"
+    )
+
+    return NfNumberEnumType(
         type="enum",
-        flavor=typ,
+        flavor="number",
         values=values,
         metadata=metadata,
-        **({"default": default} if default is not None else {}),
+        **({"default": float(default)} if default is not None else {}),
     )
 
 

src/latch_cli/services/init/init.py

@@ -379,7 +379,9 @@ def init(
 
     template_func(pkg_root)
 
-    config = get_or_create_workflow_config(pkg_root, base_image_type)
+    config = get_or_create_workflow_config(
+        pkg_root / ".latch" / "config", base_image_type
+    )
 
     wf_type = WorkflowType.latchbiosdk
     if chosen_template == "Snakemake Example":

src/latch_cli/workflow_config.py

@@ -31,9 +31,8 @@ class LatchWorkflowConfig:
 
 
 def get_or_create_workflow_config(
-    pkg_root: Path, base_image_type: BaseImageOptions = BaseImageOptions.default
+    config_path: Path, base_image_type: BaseImageOptions = BaseImageOptions.default
 ) -> LatchWorkflowConfig:
-    config_path = pkg_root / latch_constants.pkg_config
     if config_path.exists() and config_path.is_file():
         try:
             return LatchWorkflowConfig(**json.loads(config_path.read_text()))
@@ -60,9 +59,7 @@ def get_or_create_workflow_config(
         date=datetime.now(timezone.utc).isoformat(),
     )
 
-    (pkg_root / ".latch").mkdir(exist_ok=True)
-
-    with (pkg_root / latch_constants.pkg_config).open("w") as f:
-        f.write(json.dumps(asdict(config)))
+    config_path.parent.mkdir(parents=True, exist_ok=True)
+    config_path.write_text(json.dumps(asdict(config)))
 
     return config