Fix/test datasets output

CHANGELOG.md

@@ -4,6 +4,8 @@
 
 ### General
 
+- Fixes bug in `test-datasets list` related to broken rich import ([#4477](https://github.com/nf-core/tools/pull/4477))
+
 ### Linting
 
 - Warn if `manifest.diagram` is not set, and fail if it is not a relative path to an existing image file ([#4460](https://github.com/nf-core/tools/pull/4460))

nf_core/test_datasets/list.py

@@ -1,7 +1,8 @@
 import logging
 import os
 
-import rich
+from rich.console import Console
+from rich.table import Table
 
 from nf_core.test_datasets.test_datasets_utils import (
     IGNORED_FILE_PREFIXES,
@@ -14,7 +15,7 @@
 )
 from nf_core.utils import rich_force_colors
 
-stdout = rich.console.Console(force_terminal=rich_force_colors())
+stdout = Console(force_terminal=rich_force_colors())
 log = logging.getLogger(__name__)
 
 
@@ -26,7 +27,7 @@ def list_dataset_branches() -> None:
     """
     remote_branches = get_remote_branch_names()
 
-    table = rich.table.Table()
+    table = Table()
     table.add_column("Test-Dataset Branches")
     for b in remote_branches:
         table.add_row(b)
@@ -71,7 +72,7 @@ def list_datasets(
         stdout.print(os.linesep.join(out))
 
     else:
-        table = rich.table.Table()
+        table = Table()
         table.add_column("File", overflow="fold")
 
         for el in out:

nf_core/test_datasets/search.py

@@ -1,7 +1,7 @@
 import logging
 
-import rich.console
-import rich.table
+from rich.console import Console
+from rich.table import Table
 
 from nf_core.test_datasets.test_datasets_utils import (
     IGNORED_FILE_PREFIXES,
@@ -14,7 +14,7 @@
 )
 from nf_core.utils import rich_force_colors
 
-stdout = rich.console.Console(force_terminal=rich_force_colors())
+stdout = Console(force_terminal=rich_force_colors())
 log = logging.getLogger(__name__)
 
 
@@ -56,7 +56,7 @@ def search_datasets(
         stdout.print(create_pretty_nf_path(selection, branch == MODULES_BRANCH_NAME))
         stdout.print(create_download_url(branch, selection))
     else:
-        table = rich.table.Table(show_header=False)
+        table = Table(show_header=False)
         table.add_column("")
         table.add_column("", overflow="fold")
         table.add_row("File Name:", selection)

nf_core/test_datasets/test_datasets_utils.py

@@ -60,6 +60,7 @@ def get_remote_branch_names() -> list[str]:
     List all branch names on the remote github repository for test-datasets for pipelines or modules.
     """
     try:
+        branches = []  # default to return, if exception is raised
         url = GithubApiEndpoints().get_pipelines_list_url()
         response = requests.get(url)
         resp_json = response.json()
@@ -189,6 +190,9 @@ def get_or_prompt_branch(maybe_branch: str) -> tuple[str, list[str]]:
 
     else:
         all_branches = get_remote_branch_names()
+        if not all_branches:
+            log.error("Branch information for test-datasets could not be fetched.")
+            return ("", [])
 
         # Find pipeline / modules root directory
         base_dir: Path = determine_base_dir()

tests/test_datasets/test_test_datasets_list.py

@@ -0,0 +1,76 @@
+import unittest
+
+import responses
+
+from nf_core.test_datasets.list import list_datasets
+from nf_core.test_datasets.test_datasets_utils import (
+    MODULES_BRANCH_NAME,
+    GithubApiEndpoints,
+)
+
+
+def mock_get_pipelines_request(rsps: responses.RequestsMock) -> None:
+    """
+    Mock request to list pipelines
+    """
+    url = "https://raw.githubusercontent.com/nf-core/website/refs/heads/main/public/pipeline_names.json"
+    resp_json = {
+        "pipeline": [
+            "airrflow",
+            "ampliseq",
+            "atacseq",
+            "bacass",
+            "bactmap",
+        ]
+    }
+
+    # add dummy json response at given url for get request
+    rsps.add(method="GET", url=url, json=resp_json, status=200)
+
+
+def mock_gh_api_request(rsps: responses.RequestsMock, branch=MODULES_BRANCH_NAME) -> None:
+    """
+    Mock request to list files in a github branch
+    """
+    gh_urls = GithubApiEndpoints(gh_orga="nf-core", gh_repo="test-datasets")
+
+    # output from requets for modules files
+    resp_json = {
+        "sha": "bd061d2421282afa00ae1c83b43151fda0e046b7",
+        "url": "https://api.github.com/repos/nf-core/test-datasets/git/trees/bd061d2421282afa00ae1c83b43151fda0e046b7",
+        "tree": [
+            {
+                "path": "README.md",
+                "type": "blob",
+                "url": "https://api.github.com/repos/nf-core/test-datasets/git/blobs/1ebf7eb543cbb09b875a8a1ef50e107c5cfa8310",
+            },
+            {
+                "path": "assemblies",
+                "type": "tree",
+                "url": "https://api.github.com/repos/nf-core/test-datasets/git/trees/fdf5797e56e51b5e0bbd583e8499ef660204a194",
+            },
+            {
+                "path": "assemblies/MEGAHIT-test_minigut.contigs.fa.gz",
+                "type": "blob",
+                "url": "https://api.github.com/repos/nf-core/test-datasets/git/blobs/83185a06b64158a5ea144b8a5a4c26499cd3f585",
+            },
+            {
+                "path": "samplesheets/assembly_samplesheet.csv",
+                "type": "blob",
+                "url": "https://api.github.com/repos/nf-core/test-datasets/git/blobs/0b86b23c3f901103a1a72ec9953a67623cd90e3e",
+            },
+        ],
+    }
+
+    # Add dummy json response at gh url with ok status code
+    rsps.add(method="GET", url=gh_urls.get_remote_tree_url_for_branch(branch), json=resp_json, status=200)
+
+
+class TestTestDatasetsList(unittest.TestCase):
+    def test_list_datasets(self):
+        with responses.RequestsMock() as rsps:
+            branch = MODULES_BRANCH_NAME
+            mock_get_pipelines_request(rsps)
+            mock_gh_api_request(rsps, branch=branch)
+            res = list_datasets(maybe_branch=branch)
+            assert res is None