Merge pull request #308 from tkkuehn/provenance

Save more provenance information

pyproject.toml

@@ -52,6 +52,7 @@ boutiques = "^0.5.25"
 more-itertools = ">=8,<10"
 cached-property = "^1.5.2"
 pvandyken-deprecated = "0.0.3"
+importlib_metadata = [ { version = "==1.4", python = "<3.8" } ]
 
 #  Below are non-direct dependencies (i.e. dependencies of other depenencies)
 #  specified to ensure a version with a pre-built wheel is installed depending

snakebids/app.py

@@ -13,6 +13,11 @@
 import snakemake
 from snakemake.io import load_configfile
 
+if sys.version_info >= (3, 8):
+    from importlib import metadata
+else:
+    import importlib_metadata as metadata
+
 from snakebids.cli import (
     SnakebidsArgs,
     add_dynamic_args,
@@ -70,6 +75,26 @@ def wrapper(self: "SnakeBidsApp"):
     return wrapper
 
 
+def _get_app_version(self: SnakeBidsApp) -> str | None:
+    """Attempt to get the app version, returning None if we can't.
+
+    This will succeed only if the following conditions are true:
+
+    1. The Snakebids app is a distribution package installed in the current
+       environment.
+    2. The app's distribution package has the same name as this
+       SnakeBidsApp's snakemake_dir
+    """
+    try:
+        return metadata.version(self.snakemake_dir.name)
+    except metadata.PackageNotFoundError:
+        logger.warning(
+            "App version not found; will be recorded in output as 'unknown'. "
+            "If this is unexpected, please contact the app maintainer."
+        )
+        return None
+
+
 @attr.define(slots=False)
 class SnakeBidsApp:
     """Snakebids app with config and arguments.
@@ -130,6 +155,7 @@ class SnakeBidsApp:
         lambda self: load_configfile(self.snakemake_dir / self.configfile_path),
         takes_self=True,
     )
+    version: Optional[str] = attr.Factory(_get_app_version, takes_self=True)
     args: Optional[SnakebidsArgs] = None
 
     def run_snakemake(self) -> None:
@@ -207,7 +233,12 @@ def run_snakemake(self) -> None:
         # Write the config file
         write_config_file(
             config_file=new_config_file,
-            data=app.config,
+            data=dict(
+                app.config,
+                snakemake_version=metadata.version("snakemake"),
+                snakebids_version=metadata.version("snakebids"),
+                app_version=app.version or "unknown",
+            ),
             force_overwrite=True,
         )
 

snakebids/tests/test_app.py

@@ -21,6 +21,11 @@
 from ..app import SnakeBidsApp
 from .mock.config import config
 
+if sys.version_info >= (3, 8):
+    from importlib import metadata
+else:
+    import importlib_metadata as metadata
+
 
 @pytest.fixture
 def app(mocker: MockerFixture):
@@ -178,6 +183,9 @@ def test_runs_in_correct_mode(
                 "pybidsdb_reset": True,
                 "snakefile": Path("Snakefile"),
                 "output_dir": outputdir.resolve(),
+                "snakemake_version": metadata.version("snakemake"),
+                "snakebids_version": metadata.version("snakebids"),
+                "app_version": "unknown",  # not installing a snakebids app here
             }
         )
         if root == "app" and not tail:
@@ -297,6 +305,24 @@ def plugin(my_app: SnakeBidsApp):
 
         assert app.foo == "bar"  # type: ignore
 
+    def test_get_app_version_no_package(self, app: SnakeBidsApp):
+        assert app.version is None
+
+    def test_get_app_version_package(self, mocker: MockerFixture):
+        metadata_pkg = (
+            "importlib.metadata" if sys.version_info >= (3, 8) else "importlib_metadata"
+        )
+        mock = mocker.patch(f"{metadata_pkg}.version", return_value="0.1.0")
+        app = SnakeBidsApp(
+            Path("my_app"),
+            snakefile_path=Path("Snakefile"),
+            configfile_path=Path("mock/config.yaml"),
+            config=copy.deepcopy(config),
+        )
+
+        assert app.version == "0.1.0"
+        mock.assert_called_once_with("my_app")
+
 
 class TestGenBoutiques:
     def test_boutiques_descriptor(self, tmp_path: Path, app: SnakeBidsApp):