spython: add type hints

cwltool/singularity.py

@@ -8,10 +8,11 @@
 import sys
 from subprocess import check_call, check_output  # nosec
 from typing import Callable, Dict, List, MutableMapping, Optional, Tuple, cast
-from spython.main.parse.parsers import DockerParser  # type: ignore
-from spython.main.parse.writers import get_writer  # type: ignore
-from spython.main import Client  # type: ignore
+
 from schema_salad.sourceline import SourceLine
+from spython.main import Client
+from spython.main.parse.parsers.docker import DockerParser
+from spython.main.parse.writers.singularity import SingularityWriter
 
 from .builder import Builder
 from .context import RuntimeContext
@@ -180,12 +181,9 @@ def get_image(
             with open(dockerfile_path, "w") as dfile:
                 dfile.write(dockerRequirement["dockerFile"])
 
-            parser = DockerParser(dockerfile_path)
-            SingularityWriter = get_writer("singularity")
-            writer = SingularityWriter(parser.recipe)
-            result = writer.convert()
+            singularityfile = SingularityWriter(DockerParser(dockerfile_path).parse()).convert()
             with open(singularityfile_path, "w") as file:
-                file.write(result)
+                file.write(singularityfile)
 
             os.environ["APPTAINER_TMPDIR"] = absolute_path
             Client.build(recipe=singularityfile_path, build_folder=absolute_path, sudo=False)

mypy-stubs/spython/main/__init__.pyi

@@ -0,0 +1,9 @@
+from typing import Iterator, Optional
+
+from .base import Client as _BaseClient
+from .build import build as base_build
+
+class _Client(_BaseClient):
+    build = base_build
+
+Client = _Client()

mypy-stubs/spython/main/build.pyi

@@ -0,0 +1,23 @@
+from typing import Iterator, Optional
+
+from .base import Client
+
+def build(
+    self: Client,
+    recipe: Optional[str] = ...,
+    image: Optional[str] = ...,
+    isolated: Optional[bool] = ...,
+    sandbox: Optional[bool] = ...,
+    writable: Optional[bool] = ...,
+    build_folder: Optional[str] = ...,
+    robot_name: Optional[bool] = ...,
+    ext: Optional[str] = ...,
+    sudo: Optional[bool] = ...,
+    stream: Optional[bool] = ...,
+    force: Optional[bool] = ...,
+    options: Optional[list[str]] | None = ...,
+    quiet: Optional[bool] = ...,
+    return_result: Optional[bool] = ...,
+    sudo_options: Optional[str | list[str]] = ...,
+    singularity_options: Optional[list[str]] = ...,
+) -> tuple[str, Iterator[str]]: ...

mypy-stubs/spython/main/parse/parsers/base.pyi

@@ -0,0 +1,14 @@
+import abc
+
+from ..recipe import Recipe
+
+class ParserBase(metaclass=abc.ABCMeta):
+    filename: str
+    lines: list[str]
+    args: dict[str, str]
+    active_layer: str
+    active_layer_num: int
+    recipe: dict[str, Recipe]
+    def __init__(self, filename: str, load: bool = ...) -> None: ...
+    @abc.abstractmethod
+    def parse(self) -> dict[str, Recipe]: ...

mypy-stubs/spython/main/parse/parsers/docker.pyi

@@ -0,0 +1,7 @@
+from ..recipe import Recipe
+from .base import ParserBase as ParserBase
+
+class DockerParser(ParserBase):
+    name: str
+    def __init__(self, filename: str = ..., load: bool = ...) -> None: ...
+    def parse(self) -> dict[str, Recipe]: ...

mypy-stubs/spython/main/parse/recipe.pyi

@@ -0,0 +1,19 @@
+from typing import Optional
+
+class Recipe:
+    cmd: Optional[str]
+    comments: list[str]
+    entrypoint: Optional[str]
+    environ: list[str]
+    files: list[str]
+    layer_files: dict[str, str]
+    install: list[str]
+    labels: list[str]
+    ports: list[str]
+    test: Optional[str]
+    volumes: list[str]
+    workdir: Optional[str]
+    layer: int
+    fromHeader: Optional[str]
+    source: Optional[Recipe]
+    def __init__(self, recipe: Optional[Recipe] = ..., layer: int = ...) -> None: ...

mypy-stubs/spython/main/parse/writers/base.pyi

@@ -0,0 +1,6 @@
+from ..recipe import Recipe
+
+class WriterBase:
+    recipe: dict[str, Recipe]
+    def __init__(self, recipe: dict[str, Recipe] | None = ...) -> None: ...
+    def write(self, output_file: str | None = ..., force: bool = ...) -> None: ...

mypy-stubs/spython/main/parse/writers/singularity.pyi

@@ -0,0 +1,10 @@
+from typing import Optional
+
+from ..recipe import Recipe
+from .base import WriterBase as WriterBase
+
+class SingularityWriter(WriterBase):
+    name: str
+    def __init__(self, recipe: Optional[dict[str, Recipe]] = ...) -> None: ...
+    def validate(self) -> None: ...
+    def convert(self, runscript: str = ..., force: bool = ...) -> str: ...

tests/test_tmpdir.py

@@ -1,7 +1,7 @@
 """Test that all temporary directories respect the --tmpdir-prefix and --tmp-outdir-prefix options."""
+import os
 import re
 import shutil
-import os
 import subprocess
 import sys
 from pathlib import Path