Update comments

nf-core · JulianFlesch · Aug 28, 2025 · Aug 8, 2025 · Aug 8, 2025 · Aug 8, 2025
commit 7dede8a63978fc997ff9a2c5402ad79abede620f
diff --git a/tests/pipelines/download/test_docker.py b/tests/pipelines/download/test_docker.py
@@ -51,6 +51,9 @@ def test_docker_progress_pull(self):
             assert table.columns[2]._cells[0] == "([blue]Pulling)"
 
 
+#
+# Test the DockerFetcher class
+#
 class DockerTest(unittest.TestCase):
     @pytest.fixture(autouse=True)
     def use_caplog(self, caplog):
@@ -71,7 +74,7 @@ def __contains__(self, item: str) -> bool:
         return any(record.message == item for record in self._caplog.records if self._caplog)
 
     #
-    # Tests for 'DockerFetcher.pull_image'
+    # Tests for 'pull_image'
     #
     # If Docker is installed, but the container can't be accessed because it does not exist or there are access
     # restrictions, a RuntimeWarning is raised due to the unavailability of the image.
@@ -119,7 +122,7 @@ def test_docker_pull_image_docker_installed(self, tmp_dir, mock_progress, mock_t
             docker_fetcher.pull_image("ghcr.io/ewels/multiqc:go-rewrite", mock_task_obj)
 
     #
-    # Tests for 'DockerFetcher.pull_and_save_image'
+    # Tests for 'pull_and_save_image'
     #
     @pytest.mark.skipif(
         shutil.which("docker") is None,
@@ -138,7 +141,7 @@ def test_docker_pull_image_successfully(self, tmp_dir, mock_progress):
         docker_fetcher.pull_and_save_image("hello-world", tmp_dir / "hello-world.tar")
 
     #
-    # Tests for 'DockerFetcher.save_image'
+    # Tests for 'save_image'
     #
     @pytest.mark.skipif(
         shutil.which("docker") is None,
@@ -165,7 +168,7 @@ def test_docker_save_image(self, tmp_dir, mock_progress, mock_task):
 
     #
     #
-    # Tests for 'DockerFetcher.fetch_containers'
+    # Tests for 'fetch_containers': this will test fetch remote containers automatically
     #
     @pytest.mark.skipif(
         shutil.which("singularity") is None and shutil.which("apptainer") is None,
@@ -199,7 +202,7 @@ def test_fetch_containers_docker(self, tmp_path, mock_fetch_wf_config):
         )
 
     #
-    # Test for DockerFetcher.write_docker_load_command
+    # Test for 'write_docker_load_command'
     #
     def test_docker_write_docker_load_message(self):
         docker_fetcher = DockerFetcher(

diff --git a/tests/pipelines/download/test_download.py b/tests/pipelines/download/test_download.py
@@ -202,8 +202,7 @@ def test_wf_use_local_configs(self, tmp_path):
             assert wf_config["params.custom_config_base"] == f"{test_outdir}/workflow/../configs/"
 
     #
-    # Test that `find_container_images` (uses `nextflow inspect`) and `find_container_images_legacy`
-    # produces the same results
+    # Test that `find_container_images` (uses `nextflow inspect`) fetches the correct Docker images
     #
     @pytest.mark.skipif(
         shutil.which("nextflow") is None or not check_nextflow_version(NF_INSPECT_MIN_NF_VERSION),
@@ -242,8 +241,7 @@ def test_containers_pipeline_singularity(self, tmp_path, mock_fetch_wf_config):
         )
 
     #
-    # Test that `find_container_images` (uses `nextflow inspect`) and `find_container_images_legacy`
-    # produces the same results
+    # Test that `find_container_images` (uses `nextflow inspect`) fetches the correct Docker images
     #
     @pytest.mark.skipif(
         shutil.which("nextflow") is None or not check_nextflow_version(NF_INSPECT_MIN_NF_VERSION),

diff --git a/tests/pipelines/download/test_singularity.py b/tests/pipelines/download/test_singularity.py
@@ -97,6 +97,9 @@ def test_singularity_download_progress(self):
             assert table.columns[6]._cells[0]._text == ["?"]
 
 
+#
+# Test the SingularityFetcher class
+#
 class SingularityTest(unittest.TestCase):
     @pytest.fixture(autouse=True)
     def use_caplog(self, caplog):
@@ -201,7 +204,7 @@ def test_singularity_pull_image_singularity_installed(self, tmp_dir, mock_progre
 
     #
     #
-    # Tests for 'SingularityFetcher.fetch_containers'
+    # Tests for 'fetch_containers': this will test fetch remote containers automatically
     #
     @pytest.mark.skipif(
         shutil.which("singularity") is None and shutil.which("apptainer") is None,
@@ -238,7 +241,7 @@ def test_fetch_containers_singularity(self, tmp_path, mock_fetch_wf_config):
         )
 
     #
-    # Tests for 'singularity.symlink_registries' function
+    # Tests for the 'symlink_registries' function
     #
 
     # Simple file name with no registry in it
@@ -390,7 +393,7 @@ def test_symlink_singularity_symlink_registries(
             mock_open.assert_called_once_with(tmp_path / "path/to", os.O_RDONLY)
 
     #
-    # Tests for 'SingularityFetcher.pull_image'
+    # Tests for 'pull_image'
     #
     @pytest.mark.skipif(
         shutil.which("singularity") is None and shutil.which("apptainer") is None,
@@ -470,7 +473,7 @@ def test_singularity_pull_image_singularity_not_installed(self, tmp_dir, mock_ri
             fetcher.check_and_set_implementation()
 
     #
-    # Test for 'singularity.get_container_filename' function
+    # Test for 'get_container_filename' function
     #
 
     @mock.patch("nf_core.pipelines.download.singularity.SingularityFetcher.check_and_set_implementation")
@@ -586,8 +589,17 @@ def test_remote_container_functionality(self, tmp_dir):
         assert "depot.galaxyproject.org-singularity-salmon-1.5.2--h84f40af_0.img" in containers_remote
         assert "MV Rena" not in containers_remote  # decoy in test file
 
+
+#
+# Tests for the FileDownloader class
+#
+class FileDownloaderTest(unittest.TestCase):
+    @pytest.fixture(autouse=True)
+    def use_caplog(self, caplog):
+        self._caplog = caplog
+
     #
-    # Test for 'singularity.FileDownloader.download_file'
+    # Test for 'download_file'
     #
     @with_temporary_folder
     def test_file_download(self, outdir):
@@ -659,14 +671,8 @@ def test_file_download(self, outdir):
                 downloader.download_file(src_url, output_path)
             assert not (output_path).exists()
 
-
-class FileDownloaderTest(unittest.TestCase):
-    @pytest.fixture(autouse=True)
-    def use_caplog(self, caplog):
-        self._caplog = caplog
-
     #
-    # Test for 'singularity.FileDownloader.download_files_in_parallel'
+    # Test for 'download_files_in_parallel'
     #
     @with_temporary_folder
     def test_parallel_downloads(self, outdir):