feat: Add Test Data classes to download from github releases

.github/workflows/main.yml

@@ -32,8 +32,10 @@ jobs:
           locked: false # wont be the same because of the tag
 
       - name: Run pytest
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
-          pixi run -e ${{ matrix.env }} test
+          pixi run -e ${{ matrix.env }} test -s -vv
 
       - name: Upload coverage report artifact to be used by Codecov
         # only upload if matrix.os is ubuntu-latest and matrix.python-version is 3.12

README.md

@@ -1,3 +1,5 @@
+<div align="center">
+
 # Med-Imagetools: Transparent and Reproducible Medical Image Processing Pipelines in Python
 <!--intro-start-->
 
@@ -15,6 +17,8 @@
 [![PyPI - Format](https://img.shields.io/pypi/format/med-imagetools)](https://pypi.org/project/med-imagetools/)
 [![Downloads](https://static.pepy.tech/badge/med-imagetools)](https://pepy.tech/project/med-imagetools)
 
+</div>
+
 ## Med-ImageTools core features
 
 * AutoPipeline CLI

pixi.toml

@@ -3,7 +3,7 @@ authors = ["Jermiah Joseph <jermiahjoseph98@gmail.com>"]
 channels = ["conda-forge"]
 description = "Add a short description here"
 name = "med-imagetools"
-platforms = ["linux-64", "osx-arm64"]
+platforms = ["linux-64", "osx-arm64", "osx-64"]
 
 
 [dependencies]
@@ -12,7 +12,7 @@ pip = ">=24.3.1,<25"
 
 
 [pypi-dependencies]
-med-imagetools = { path = ".", editable = true }
+med-imagetools = { path = ".", editable = true}
 
 [environments]
 dev = ["test", "quality", "build", "dev", "docs"]
@@ -23,6 +23,9 @@ py311 = { features = ["py311", "test"], no-default-feature = true }
 py312 = { features = ["py312", "test"], no-default-feature = true }
 
 ############################################## DEV ###############################################
+[feature.dev.pypi-dependencies]
+med-imagetools = { path = ".", editable = true, extras = ["all"]}
+
 [feature.dev.dependencies]
 ipython = "*"
 ipykernel = "*"
@@ -47,18 +50,17 @@ python = "3.11.*"
 [feature.py312.dependencies]
 python = "3.12.*"
 
-
 ############################################## TEST ################################################
+[feature.test.pypi-dependencies]
+med-imagetools = { path = ".", editable = true, extras = ["test"]}
 
 [feature.test.dependencies]
 pytest = "*"
 pytest-cov = "*"
-pytest-xdist = "*"
+# pytest-xdist = "*" re-introduce later. 
 pytest-mock = ">=3.14.0,<4"
 sqlalchemy-stubs = ">=0.4,<0.5"
 
-[feature.test.pypi-dependencies]
-med-imagetools = { path = ".", editable = true }
 
 [feature.test.tasks.test]
 cmd = "pytest -c config/pytest.ini --rootdir ."

pyproject.toml

@@ -54,7 +54,17 @@ classifiers = [
 # Optional dependencies (extras)
 [project.optional-dependencies]
 torch = ["torch", "torchio"]
-debug = ["pyvis"]
+test = [
+  "pygithub>=2.5.0",
+  "aiohttp>=3.8.1",
+]
+all = [
+  "pygithub>=2.5.0",
+  # add these back later
+  # "torch",
+  # "torchio",
+]
+# debug = ["pyvis"]
 
 # Entry points for CLI commands
 [project.scripts]

src/imgtools/cli/__main__.py

@@ -5,6 +5,7 @@
 from . import set_log_verbosity
 from .dicomfind import find_dicoms
 from .dicomsort import dicomsort
+from .testdatasets import is_testdata_available
 
 
 @click.group(
@@ -29,5 +30,10 @@ def cli(verbose: int, quiet: bool) -> None:
 cli.add_command(dicomsort)
 cli.add_command(find_dicoms, "find-dicoms")
 
+if is_testdata_available():
+    from .testdatasets import testdata
+
+    cli.add_command(testdata)
+
 if __name__ == "__main__":
     cli()

src/imgtools/cli/testdatasets.py

@@ -0,0 +1,73 @@
+import pathlib
+from typing import List
+
+import click
+
+
+def is_testdata_available() -> bool:
+    try:
+        from github import Github  # type: ignore # noqa
+
+        return True
+    except ImportError:
+        return False
+
+
+if is_testdata_available():
+    from imgtools.datasets import MedImageTestData
+
+
+@click.command()
+@click.argument(
+    "dest",
+    type=click.Path(
+        exists=False,
+        file_okay=False,
+        dir_okay=True,
+        writable=True,
+        path_type=pathlib.Path,
+        resolve_path=True,
+    ),
+)
+@click.option(
+    "-a",
+    "--assets",
+    multiple=True,
+    help="Specific assets to download. If not provided, all assets will be downloaded.",
+)
+@click.help_option(
+    "-h",
+    "--help",
+)
+def testdata(dest: pathlib.Path, assets: List[str]) -> None:
+    """Download test data from the latest GitHub release.
+
+    DEST is the directory where the test data will be saved.
+
+    assets can be one of the following:
+
+    \b
+    - 4D-Lung.tar.gz
+    - CC-Tumor-Heterogeneity.tar.gz
+    - NSCLC-Radiomics.tar.gz
+    - NSCLC_Radiogenomics.tar.gz
+    - QIN-PROSTATE-Repeatability.tar.gz
+    - Soft-tissue-Sarcoma.tar.gz
+    - Vestibular-Schwannoma-SEG.tar.gz
+
+    """
+    manager = MedImageTestData()
+    selected_assets = None
+
+    if assets:
+        selected_assets = [asset for asset in manager.datasets if asset.name in assets]
+        if not selected_assets:
+            click.echo(f"No matching assets found for: {', '.join(assets)}")
+            return
+
+    downloaded_files = manager.download(dest, assets=selected_assets)
+    click.echo(f"Downloaded files: {', '.join(str(file) for file in downloaded_files)}")
+
+
+if __name__ == "__main__":
+    testdata()

src/imgtools/datasets/__init__.py

@@ -0,0 +1,13 @@
+from .github_helper import (
+    GitHubRelease,
+    GitHubReleaseAsset,
+    GitHubReleaseManager,
+    MedImageTestData,
+)
+
+__all__ = [
+    "GitHubRelease",
+    "GitHubReleaseAsset",
+    "GitHubReleaseManager",
+    "MedImageTestData",
+]