feat(tests): add test dataset downloading and extraction helpers (#201)

## Release Notes

- **New Features**
- Enhanced dataset downloading functionality with progress tracking and
timeout management
	- Improved dataset extraction with parallel processing support

- **Improvements**
	- Refined GitHub release management
	- Updated test data handling and fixtures
	- Improved logging and error handling for dataset operations

- **Changes**
	- Renamed `GitHubReleaseManager` to `MedImageTestData`
	- Updated variable names for better clarity in various modules
	- Adjusted DICOM file saving parameters

- **Testing**
	- Added new test cases for dataset integrity and download processes
	- Enhanced type annotations and test fixtures

Author: jjjermiah

devnotes/testing.md

@@ -0,0 +1,29 @@
+# Testing Information
+
+Med-imagetools uses the `pytest` framework with `pixi`
+to assist with testing, and `coverage` to measure test coverage.
+
+Mainly, being able to run a test suite across a matrix of
+python environments in CI/CD automatically.
+
+See the `test` feature in the `pixi.toml` file for the
+dependencies, and tasks.
+
+## Data
+
+As of January 2025, the test data is downloaded from the
+[`bhklab/med-image_test-data`](https://github.com/bhklab/med-image_test-data)
+which is an automated pipeline that uses `snakemake` to query,
+download and prepare the data. The pipeline is run on
+GitHub Actions, and the data is uploaded to the `releases`
+section of the repository where it is then sourced by
+many packages.
+
+Med-Imagetools has an interface in `src/imgtools/datasets` that
+can be used to download the data, and prepare it for testing.
+If users want to use the data, they need to install the package with
+`med-imagetools[test]` so it has the dependencies to download the data.
+
+our `pixi` configuration includes the optional-dependencies for the entire
+package so we dont have to worry much about it.
+

pixi.lock

@@ -61,10 +61,8 @@ pytest-cov = "*"
 pytest-mock = ">=3.14.0,<4"
 sqlalchemy-stubs = ">=0.4,<0.5"
 
-
 [feature.test.tasks.test]
 cmd = "pytest -c config/pytest.ini --rootdir . --basetemp='./tests/temp'"
-inputs = ["src", "tests", "config/pytest.ini", "config/coverage.toml"]
 description = "Run pytest (make sure to run in root directory)"
 
 [feature.test.tasks.test_ci]
@@ -77,7 +75,7 @@ depends-on = ["test"]
 description = "Run pytest and generate coverage report"
 
 [feature.test.tasks.clean_tests]
-cmd = "rm -rf .pytest_cache data tests/temp temp_outputs"
+cmd = "rm -rf .pytest_cache data tests/temp temp_outputs .cache"
 ############################################## DOCS ###############################################
 [feature.docs.dependencies]
 mkdocs = "*"

pixi.toml

@@ -81,9 +81,14 @@ requires = ["hatchling"]
 directory = "dist"
 
 [tool.hatch.build.targets.wheel]
+# Automatically discovers packages in `src/`
 packages = ["src/imgtools"]
-include = ["pyproject.toml", "README.md", "src/**"]
-
+include = [
+    "pyproject.toml",
+    "README.md",
+    "src/imgtools/py.typed",
+    "src/**"
+]
 
 [tool.semantic_release]
 version_variables = ["src/imgtools/__init__.py:__version__"]

pyproject.toml

@@ -1,13 +1,11 @@
 from .github_helper import (
     GitHubRelease,
     GitHubReleaseAsset,
-    GitHubReleaseManager,
     MedImageTestData,
 )
 
 __all__ = [
     "GitHubRelease",
     "GitHubReleaseAsset",
-    "GitHubReleaseManager",
     "MedImageTestData",
 ]