Test Command (#11)

* Updated _image.py to a new version

* Added the "Test" command

* Fixed most of the test failures, probably not a final fix

* Documentation fixes per PR

+ Exposed `default_user` to the CLI for `dropin` command
~ Changed `test` to mount to the parent of the given logfile instead of a hard-coded location
~ Changed `logfile` under `test` to `output_xml`
~ Changed some imports and type annotations to fit `__future__.annotations`

* Updated lockfiles to avoid hdf5 1.14.2 dependency

* Added the test test, fixed test, tested test (success!)

* Testing container mount moved from `/temporary/Testing` to `/scratch/Testing`.

---------

Co-authored-by: tyler-g-hudson <[email protected]>

Author: Tyler-g-hudson

env_files/lock-dev.txt

@@ -1,6 +1,7 @@
 import re
 from pathlib import Path
 from subprocess import PIPE
+from tempfile import TemporaryDirectory
 from typing import Dict, Iterator, Tuple
 
 from pytest import fixture, mark
@@ -11,6 +12,7 @@
     cmake_config_dockerfile,
     cmake_install_dockerfile,
 )
+from wigwam.commands import test as command_test
 
 from .utils import (
     determine_scope,
@@ -289,3 +291,20 @@ def test_cmake_install_image(
             """
             isce3_cmake_install_image.run(command='python -c "import isce3"')
             isce3_cmake_install_image.run(command='python -c "import nisar"')
+
+        @mark.isce3
+        @mark.slow
+        def test_test_command(
+            self,
+            isce3_cmake_install_tag: str,
+            isce3_cmake_install_image: Image,  # type: ignore
+        ):
+            with TemporaryDirectory() as temp_dir:
+                output_xml = Path(temp_dir) / "temp.xml"
+                command_test(
+                    tag=isce3_cmake_install_tag,
+                    output_xml=output_xml,
+                    compress_output=False,
+                    quiet_fail=False,
+                )
+                assert output_xml.is_file()

env_files/lock-runtime.txt

@@ -38,10 +38,10 @@ def cmake_config_dockerfile(base: str, build_type: str, with_cuda: bool = True)
     cmake_extra_args = " ".join(additional_args)
 
     # Begin constructing the dockerfile with the initial FROM line.
-    dockerfile: str = f"FROM {base}\n\n"
+    dockerfile: str = f"FROM {base}"
 
     # Activate the micromamba user and environment.
-    dockerfile += micromamba_docker_lines() + "\n\n"
+    dockerfile += f"\n\n{micromamba_docker_lines()}\n\n"
     dockerfile += dedent(
         f"""
             ENV INSTALL_PREFIX {str(install_prefix())}
@@ -59,6 +59,7 @@ def cmake_config_dockerfile(base: str, build_type: str, with_cuda: bool = True)
         """
     ).strip()
 
+    dockerfile += "\n"
     return dockerfile
 
 
@@ -77,14 +78,19 @@ def cmake_build_dockerfile(base: str) -> str:
         The generated Dockerfile.
     """
     # Begin constructing the dockerfile with the initial FROM line.
-    dockerfile = f"FROM {base}\n\n"
+    dockerfile = f"FROM {base}"
 
     # Run as the $MAMBA_USER and activate the micromamba environment.
-    dockerfile += f"{micromamba_docker_lines()}\n\n"
+    dockerfile += f"\n\n{micromamba_docker_lines()}"
 
     # Build the project.
-    dockerfile += "RUN cmake --build $BUILD_PREFIX --parallel"
+    dockerfile += "\n\nRUN cmake --build $BUILD_PREFIX --parallel"
 
+    # Add permissions to the testing subdirectory under the build prefix.
+    # This step is necessary to enable testing on the image.
+    dockerfile += "\n\nRUN chmod -R 777 $BUILD_PREFIX"
+
+    dockerfile += "\n"
     return dockerfile
 
 
@@ -103,10 +109,10 @@ def cmake_install_dockerfile(base: str) -> str:
         The generated Dockerfile.
     """
     # Begin constructing the dockerfile with the initial FROM line.
-    dockerfile = f"FROM {base}\n\n"
+    dockerfile = f"FROM {base}"
 
     # Run as the $MAMBA_USER and activate the micromamba environment.
-    dockerfile += f"{micromamba_docker_lines()}\n\n"
+    dockerfile += f"\n\n{micromamba_docker_lines()}\n\n"
 
     # Install the project and set the appropriate permissions at the target directory.
     dockerfile += dedent(
@@ -129,4 +135,5 @@ def cmake_install_dockerfile(base: str) -> str:
         """
     ).strip()
 
+    dockerfile += "\n"
     return dockerfile

test/test_docker_cmake.py

@@ -1,10 +1,14 @@
+from __future__ import annotations
+
 import io
 import os
+from collections.abc import Iterable
 from shlex import split
 from subprocess import DEVNULL, CalledProcessError, run
 from sys import stdin
-from typing import Any, List, Optional, Type, TypeVar, Union, overload
+from typing import Any, Type, TypeVar, overload
 
+from ._bind_mount import BindMount
 from ._exceptions import CommandNotFoundError, DockerBuildError, ImageNotFoundError
 
 
@@ -16,7 +20,7 @@ class Image:
     an interface by which to interact with that image.
 
     Capabilities include:
-    -   Building Docker images from dockerfiles or Dockerfile-formatted strings
+    -   Building Docker images from Dockerfiles or Dockerfile-formatted strings
         via :func:`~wigwam.Image.build`.
     -   Running commands in containers built from the image using
         :func:`~wigwam.Image.run`.
@@ -42,8 +46,8 @@ def build(
         cls: Type[Self],
         tag: str,
         *,
-        dockerfile: Union[str, os.PathLike[str]],
-        context: Union[str, os.PathLike[str]] = ...,
+        dockerfile: os.PathLike[str] | str,
+        context: os.PathLike[str] | str = ...,
         stdout: Any = ...,
         stderr: Any = ...,
         network: str = ...,
@@ -60,8 +64,7 @@ def build(
         tag : str
             A name for the image.
         dockerfile : os.PathLike
-            The path of the Dockerfile to build
-            directory.
+            The path of the Dockerfile to build directory.
         context : os.PathLike, optional
             The build context. Defaults to ".".
         stdout : io.TextIOBase or special value, optional
@@ -95,7 +98,7 @@ def build(
         tag: str,
         *,
         dockerfile_string: str,
-        context: Union[str, os.PathLike[str]] = ...,
+        context: os.PathLike[str] | str = ...,
         stdout: Any = ...,
         stderr: Any = ...,
         network: str = ...,
@@ -132,7 +135,7 @@ def build(
         DockerBuildError
             If the Docker build command fails.
         ValueError
-            If both `Dockerfile` and `dockerfile_string` are defined.
+            If both `dockerfile` and `dockerfile_string` are defined.
         """
         ...
 
@@ -194,14 +197,14 @@ def build(
 
         return cls(tag)
 
-    def _inspect(self, format: Optional[str] = None) -> str:
+    def _inspect(self, format: str | None = None) -> str:
         """
         Use 'docker inspect' to retrieve a piece of information about the
         image.
 
         Parameters
         ----------
-        format : str, optional
+        format : str or None, optional
             The value to be requested by the --format argument, or None.
             Defaults to None.
 
@@ -224,11 +227,13 @@ def run(
         self,
         command: str,
         *,
-        stdout: Optional[Union[io.TextIOBase, int]] = None,
-        stderr: Optional[Union[io.TextIOBase, int]] = None,
+        stdout: io.TextIOBase | int | None = None,
+        stderr: io.TextIOBase | int | None = None,
         interactive: bool = False,
         network: str = "host",
         check: bool = True,
+        host_user: bool = False,
+        bind_mounts: Iterable[BindMount] | None = None,
     ) -> str:
         """
         Run the given command on a container.
@@ -253,6 +258,11 @@ def run(
         check: bool, optional
             If True, check for CalledProcessErrors on non-zero return codes. Defualts
             to True.
+        host_user: bool, optional
+            If True, run the command as the user on the host machine, else run as the
+            default user. Defaults to False.
+        bind_mounts : Iterable[BindMount], optional
+            A list of bind mount descriptions to apply to the run command.
 
         Returns
         -------
@@ -264,7 +274,13 @@ def run(
         CommandNotFoundError:
             When a command is attempted that is not recognized on the image.
         """
+
         cmd = ["docker", "run", f"--network={network}", "--rm"]
+        if host_user:
+            cmd += ["-u", f"{os.getuid()}:{os.getgid()}"]
+        if bind_mounts is not None:
+            for mount in bind_mounts:
+                cmd += ["-v", f"{mount.mount_string()}"]
         if interactive:
             cmd += ["-i"]
             if stdin.isatty():
@@ -288,7 +304,7 @@ def run(
                 raise
         return result.stdout
 
-    def drop_in(self, network: str = "host") -> None:
+    def drop_in(self, network: str = "host", host_user: bool = True) -> None:
         """
         Start a drop-in session on a disposable container.
 
@@ -300,15 +316,18 @@ def drop_in(self, network: str = "host") -> None:
         ----------
         network : str, optional
             The name of the network. Defaults to "host".
+        host_user: bool, optional
+            If True, run as the current user on the host machine. Else, run as the
+            default user in the image. Defaults to True.
 
         Raises
         -------
         CommandNotFoundError:
             When bash is not recognized on the image.
         """
-        self.run(
-            "bash", interactive=True, network=network, check=False
-        )  # pragma: no cover
+        self.run(  # pragma: no cover
+            "bash", interactive=True, network=network, check=False, host_user=host_user
+        )
 
     def has_command(self, command: str) -> bool:
         """
@@ -339,8 +358,8 @@ def has_command(self, command: str) -> bool:
             return True
 
     @property
-    def tags(self) -> List[str]:
-        """List[str]: The Repo Tags held on this Docker image."""
+    def tags(self) -> list[str]:
+        """list[str]: The Repo Tags held on this Docker image."""
         return self._inspect(format="{{.RepoTags}}").strip("][\n").split(", ")
 
     @property

wigwam/_docker_cmake.py

@@ -2,7 +2,7 @@
 
 import argparse
 
-from ..commands import dropin, make_lockfile, remove
+from ..commands import dropin, make_lockfile, remove, test
 from ._utils import help_formatter
 
 
@@ -18,12 +18,38 @@ def init_util_parsers(subparsers: argparse._SubParsersAction, prefix: str) -> No
         The image tag prefix.
     """
 
+    test_parser = subparsers.add_parser(
+        "test", help="Run unit tests on an image.", formatter_class=help_formatter
+    )
+    test_parser.add_argument(
+        "tag", metavar="IMAGE_TAG", type=str, help="The tag or ID of the test image."
+    )
+    test_parser.add_argument(
+        "--output-xml",
+        "-o",
+        type=str,
+        default="Test.xml",
+        help="The output XML file to write test results to.",
+    )
+    test_parser.add_argument(
+        "--compress-output", action="store_true", help="Compress ctest output."
+    )
+    test_parser.add_argument(
+        "--quiet-fail", action="store_true", help="Less verbose output on test failure."
+    )
+
     dropin_parser = subparsers.add_parser(
         "dropin", help="Start a drop-in session.", formatter_class=help_formatter
     )
     dropin_parser.add_argument(
         "tag", metavar="IMAGE_TAG", type=str, help="The tag or ID of the desired image."
     )
+    test_parser.add_argument(
+        "--default-user",
+        action="store_true",
+        help="Run as the default user on the image. If not used, will run as the "
+        "current user on the host machine.",
+    )
 
     remove_parser = subparsers.add_parser(
         "remove",
@@ -93,3 +119,5 @@ def run_util(args: argparse.Namespace, command: str) -> None:
         remove(**vars(args))
     elif command == "lockfile":
         make_lockfile(**vars(args))
+    elif command == "test":
+        test(**vars(args))