Merge pull request nf-core#2529 from mashehu/mv-set_wd

move set_wd from tests/utils.py to utils.py

nf_core/components/components_test.py

@@ -19,7 +19,6 @@
 
 import nf_core.utils
 from nf_core.components.components_command import ComponentCommand
-from tests.utils import set_wd
 
 log = logging.getLogger(__name__)
 
@@ -92,7 +91,7 @@ def run(self) -> None:
         os.environ[
             "NFT_DIFF_ARGS"
         ] = "--line-numbers --expand-tabs=2"  # taken from https://code.askimed.com/nf-test/docs/assertions/snapshots/#snapshot-differences
-        with set_wd(Path(self.dir)):
+        with nf_core.utils.set_wd(Path(self.dir)):
             self.check_snapshot_stability()
         if len(self.errors) > 0:
             errors = "\n - ".join(self.errors)

nf_core/utils.py

@@ -16,8 +16,9 @@
 import subprocess
 import sys
 import time
+from contextlib import contextmanager
 from pathlib import Path
-from typing import Tuple, Union
+from typing import Generator, Tuple, Union
 
 import git
 import prompt_toolkit
@@ -1147,3 +1148,21 @@ def validate_file_md5(file_name, expected_md5hex):
         raise IOError(f"{file_name} md5 does not match remote: {expected_md5hex} - {file_md5hex}")
 
     return True
+
+
+@contextmanager
+def set_wd(path: Path) -> Generator[None, None, None]:
+    """Sets the working directory for this context.
+
+    Arguments
+    ---------
+
+    path : Path
+        Path to the working directory to be used inside this context.
+    """
+    start_wd = Path().absolute()
+    os.chdir(Path(path).resolve())
+    try:
+        yield
+    finally:
+        os.chdir(start_wd)

tests/components/generate_snapshot.py

@@ -6,8 +6,9 @@
 import pytest
 
 from nf_core.components.components_test import ComponentsTest
+from nf_core.utils import set_wd
 
-from ..utils import GITLAB_NFTEST_BRANCH, GITLAB_URL, set_wd
+from ..utils import GITLAB_NFTEST_BRANCH, GITLAB_URL
 
 
 def test_generate_snapshot_module(self):

tests/components/snapshot_test.py

@@ -5,8 +5,7 @@
 import pytest
 
 from nf_core.components.components_test import ComponentsTest
-
-from ..utils import set_wd
+from nf_core.utils import set_wd
 
 
 def test_components_test_check_inputs(self):

tests/modules/lint.py

@@ -5,8 +5,9 @@
 
 import nf_core.modules
 from nf_core.modules.lint import main_nf
+from nf_core.utils import set_wd
 
-from ..utils import GITLAB_URL, set_wd
+from ..utils import GITLAB_URL
 from .patch import BISMARK_ALIGN, CORRECT_SHA, PATCH_BRANCH, REPO_NAME, modify_main_nf
 
 

tests/test_test_utils.py

@@ -3,7 +3,7 @@
 
 import pytest
 
-from .utils import set_wd, with_temporary_file, with_temporary_folder
+from .utils import with_temporary_file, with_temporary_folder
 
 
 def test_with_temporary_file():
@@ -30,20 +30,3 @@ def tmp_folder_exists(tmp_folder):
 def test_tmp_folder_does_not_exist_after():
     tmp_folder = with_temporary_folder(lambda x: x)()
     assert not Path(tmp_folder).exists()
-
-
-def test_set_wd():
-    with tempfile.TemporaryDirectory() as tmpdirname:
-        with set_wd(tmpdirname):
-            context_wd = Path().resolve()
-        assert context_wd == Path(tmpdirname).resolve()
-        assert context_wd != Path().resolve()
-
-
-def test_set_wd_revert_on_raise():
-    wd_before_context = Path().resolve()
-    with tempfile.TemporaryDirectory() as tmpdirname:
-        with pytest.raises(Exception):
-            with set_wd(tmpdirname):
-                raise Exception
-    assert wd_before_context == Path().resolve()

tests/test_utils.py

@@ -207,3 +207,20 @@ def test_validate_file_md5():
         nf_core.utils.validate_file_md5(test_file, different_md5)
     with pytest.raises(ValueError):
         nf_core.utils.validate_file_md5(test_file, non_hex_string)
+
+
+def test_set_wd():
+    with tempfile.TemporaryDirectory() as tmpdirname:
+        with nf_core.utils.set_wd(tmpdirname):
+            context_wd = Path().resolve()
+        assert context_wd == Path(tmpdirname).resolve()
+        assert context_wd != Path().resolve()
+
+
+def test_set_wd_revert_on_raise():
+    wd_before_context = Path().resolve()
+    with tempfile.TemporaryDirectory() as tmpdirname:
+        with pytest.raises(Exception):
+            with nf_core.utils.set_wd(tmpdirname):
+                raise Exception
+    assert wd_before_context == Path().resolve()

tests/utils.py

@@ -59,24 +59,6 @@ def wrapper(*args: Any, **kwargs: Any) -> Any:
     return wrapper
 
 
-@contextmanager
-def set_wd(path: Path) -> Generator[None, None, None]:
-    """Sets the working directory for this context.
-
-    Arguments
-    ---------
-
-    path : Path
-        Path to the working directory to be used iside this context.
-    """
-    start_wd = Path().absolute()
-    os.chdir(Path(path).resolve())
-    try:
-        yield
-    finally:
-        os.chdir(start_wd)
-
-
 def mock_anaconda_api_calls(rsps: responses.RequestsMock, module: str, version: str) -> None:
     """Mock anaconda api calls for module"""
     anaconda_api_url = f"https://api.anaconda.org/package/bioconda/{module}"