Moved all singularity-related download functions into a new file

nf_core/pipelines/downloads/singularity.py

@@ -86,7 +86,7 @@ def symlink_registries(self, image_path: str) -> None:
         The base image, e.g. ./nf-core-gatk-4.4.0.0.img will thus be symlinked as for example ./quay.io-nf-core-gatk-4.4.0.0.img
         by prepending all registries in registry_set to the image name.
 
-        Unfortunately, out output image name may contain a registry definition (Singularity image pulled from depot.galaxyproject.org
+        Unfortunately, the output image name may contain a registry definition (Singularity image pulled from depot.galaxyproject.org
         or older pipeline version, where the docker registry was part of the image name in the modules). Hence, it must be stripped
         before to ensure that it is really the base name.
         """

tests/pipelines/test_download.py

@@ -632,12 +632,12 @@ def test_symlink_singularity_images(
 
         # Call the method
         singularity_fetcher = SingularityFetcher(
+            [],
             (
                 "quay.io",
                 "community-cr-prod.seqera.io/docker/registry/v2",
                 "depot.galaxyproject.org/singularity",
             ),
-            [],
             mock_rich_progress,
         )
         singularity_fetcher.symlink_registries(f"{tmp_path}/path/to/singularity-image.img")
@@ -696,41 +696,29 @@ def test_symlink_singularity_images_registry(
         mock_open.return_value = 12  # file descriptor
         mock_close.return_value = 12  # file descriptor
 
-        download_obj = DownloadWorkflow(
-            pipeline="dummy",
-            outdir=tmp_path,
-            container_library=("quay.io", "community-cr-prod.seqera.io/docker/registry/v2"),
-        )
-
-        download_obj.registry_set = {"quay.io", "community-cr-prod.seqera.io/docker/registry/v2"}
-
-        # Call the method with registry - should not happen, but preserve it then.
+        # Call the method with registry name included - should not happen, but preserve it then.
         singularity_fetcher = SingularityFetcher(
+            [],
             (
-                "quay.io",
+                "quay.io",  # Same as in the filename
                 "community-cr-prod.seqera.io/docker/registry/v2",
-                "depot.galaxyproject.org/singularity",
             ),
-            [],
             mock_rich_progress,
         )
         singularity_fetcher.symlink_registries(f"{tmp_path}/path/to/quay.io-singularity-image.img")
-        print(mock_resub.call_args)
 
         # Check that os.makedirs was called with the correct arguments
-        # mock_makedirs.assert_any_call(f"{tmp_path}/path/to", exist_ok=True)
+        mock_makedirs.assert_called_once_with(f"{tmp_path}/path/to", exist_ok=True)
 
         # Check that os.symlink was called with the correct arguments
-        mock_symlink.assert_called_with(
+        # assert_called_once_with also tells us that there was no attempt to
+        # - symlink to itself
+        # - symlink to the same registry
+        mock_symlink.assert_called_once_with(
             "./quay.io-singularity-image.img",
-            "./community-cr-prod.seqera.io-docker-registry-v2-singularity-image.img",
+            "./community-cr-prod.seqera.io-docker-registry-v2-singularity-image.img",  # "quay.io-" has been trimmed
             dir_fd=12,
         )
-        # Check that there is no attempt to symlink to itself (test parameters would result in that behavior if not checked in the function)
-        assert (
-            unittest.mock.call("./quay.io-singularity-image.img", "./quay.io-singularity-image.img", dir_fd=12)
-            not in mock_symlink.call_args_list
-        )
 
         # Normally it would be called for each registry, but since quay.io is part of the name, it
         # will only be called once, as no symlink to itself must be created.