Merge branch 'main' into list_candidates

.github/workflows/ci.yml

@@ -94,7 +94,7 @@ jobs:
           poetry run python tests/test_fake_gcs.py
 
       - name: Run pytest
-        run: poetry run coverage run -m pytest tests/tests.py
+        run: poetry run coverage run -m pytest -v tests/tests.py
 
       - name: Run Coverage
         run: poetry run coverage report -m

CHANGELOG.md

@@ -1,5 +1,22 @@
 # Changelog
 
+## [1.0.0](https://github.com/snakemake/snakemake-storage-plugin-gcs/compare/v0.1.4...v1.0.0) (2024-04-26)
+
+
+### ⚠ BREAKING CHANGES
+
+* expect correct google cloud storage abbreviation in query scheme (gcs://) ([#39](https://github.com/snakemake/snakemake-storage-plugin-gcs/issues/39))
+
+### Bug Fixes
+
+* expect correct google cloud storage abbreviation in query scheme (gcs://) ([#39](https://github.com/snakemake/snakemake-storage-plugin-gcs/issues/39)) ([0ebf52c](https://github.com/snakemake/snakemake-storage-plugin-gcs/commit/0ebf52cc6131fe092f638306f104e4c37a88aac4))
+* fix directory support ([#38](https://github.com/snakemake/snakemake-storage-plugin-gcs/issues/38)) ([ce3d165](https://github.com/snakemake/snakemake-storage-plugin-gcs/commit/ce3d165f94e2d9d8f9469434d88edc0fe1b7f2a1))
+
+
+### Documentation
+
+* add intro, fix link ([6ec568a](https://github.com/snakemake/snakemake-storage-plugin-gcs/commit/6ec568a092aa6b636549a48fc09f0f1ba07b6f00))
+
 ## [0.1.4](https://github.com/snakemake/snakemake-storage-plugin-gcs/compare/v0.1.3...v0.1.4) (2024-03-08)
 
 

README.md

@@ -1,7 +1,7 @@
 # Snakemake storage plugin: gcs
 
 A snakemake storage plugin for Google Cloud Storage.
-For documentation and usage instructions, see the [Snakemake plugin catalog](https://snakemake.github.io/snakemake-plugin-catalog/plugins/storage/s3.html).
+For documentation and usage instructions, see the [Snakemake plugin catalog](https://snakemake.github.io/snakemake-plugin-catalog/plugins/storage/gcs.html).
 
 ## Testing
 Set up a fake gcs server from [fake-gcs-server](https://github.com/fsouza/fake-gcs-server).

docs/intro.md

@@ -0,0 +1 @@
+A Snakemake storage plugin that reads and writes from [Google cloud storage (GCS)](https://cloud.google.com/storage).

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "snakemake-storage-plugin-gcs"
-version = "0.1.4"
+version = "1.0.0"
 description = "A Snakemake storage plugin for Google Cloud Storage"
 authors = [
     "Vanessa Sochat <[email protected]>",

snakemake_storage_plugin_gcs/__init__.py

@@ -192,11 +192,11 @@ def is_valid_query(cls, query: str) -> StorageQueryValidationResult:
                 valid=False,
                 reason=f"cannot be parsed as URL ({e})",
             )
-        if parsed.scheme != "gs":
+        if parsed.scheme != "gcs":
             return StorageQueryValidationResult(
                 query=query,
                 valid=False,
-                reason="must start with gs (gs://...)",
+                reason="must start with gcs scheme (gcs://...)",
             )
         return StorageQueryValidationResult(
             query=query,
@@ -210,7 +210,7 @@ def example_queries(cls) -> List[ExampleQuery]:
         """
         return [
             ExampleQuery(
-                query="gs://mybucket/myfile.txt",
+                query="gcs://mybucket/myfile.txt",
                 type=QueryType.ANY,
                 description="A file in an google storage (GCS) bucket",
             )
@@ -341,7 +341,11 @@ def get_mtime(blob):
             return blob.updated.timestamp()
 
         if self.is_directory():
-            return max(get_mtime(blob) for blob in self.directory_entries())
+            entries = list(self.directory_entries())
+            assert (
+                entries
+            ), f"bug: mtime called but directory does not seem to exist: {self.query}"
+            return max(get_mtime(blob) for blob in entries)
         else:
             return get_mtime(self.blob)
 

tests/tests.py

@@ -20,14 +20,15 @@
 
 class TestStorage(TestStorageBase):
     __test__ = True
+    files_only = False
 
     def get_query(self, tmp_path) -> str:
-        return "gs://snakemake-test-bucket/test-file.txt"
+        return "gcs://snakemake-test-bucket/test-file.txt"
 
     def get_query_not_existing(self, tmp_path) -> str:
         bucket = uuid.uuid4().hex
         key = uuid.uuid4().hex
-        return f"gs://{bucket}/{key}"
+        return f"gcs://{bucket}/{key}"
 
     def get_storage_provider_cls(self) -> Type[StorageProviderBase]:
         # Return the StorageProvider class of this plugin