Merge pull request #1819 from fabianegli/use-context-when-changing-wo…

…rking-directory-in-tests

Use a context to temporarily change the working directory

CHANGELOG.md

@@ -14,6 +14,7 @@
 ### General
 
 - Add function to enable chat notifications on MS Teams, accompanied by `hook_url` param to enable it.
+- Use contextlib to temporarily change working directories ([#1819](https://github.com/nf-core/tools/pull/1819))
 
 ### Modules
 

tests/modules/lint.py

@@ -4,7 +4,7 @@
 
 import nf_core.modules
 
-from ..utils import GITLAB_URL
+from ..utils import GITLAB_URL, set_wd
 from .patch import BISMARK_ALIGN, PATCH_BRANCH, setup_patch
 
 
@@ -65,11 +65,9 @@ def test_modules_lint_patched_modules(self):
 
     # change temporarily working directory to the pipeline directory
     # to avoid error from try_apply_patch() during linting
-    wd_old = os.getcwd()
-    os.chdir(self.pipeline_dir)
-    module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir, remote_url=GITLAB_URL)
-    module_lint.lint(print_results=False, all_modules=True)
-    os.chdir(wd_old)
+    with set_wd(self.pipeline_dir):
+        module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir, remote_url=GITLAB_URL)
+        module_lint.lint(print_results=False, all_modules=True)
 
     assert len(module_lint.failed) == 0
     assert len(module_lint.passed) > 0

tests/modules/module_test.py

@@ -7,39 +7,35 @@
 
 import nf_core.modules
 
+from ..utils import set_wd
+
 
 def test_modules_test_check_inputs(self):
     """Test the check_inputs() function - raise UserWarning because module doesn't exist"""
-    cwd = os.getcwd()
-    os.chdir(self.nfcore_modules)
-    meta_builder = nf_core.modules.ModulesTest("none", True, "")
-    with pytest.raises(UserWarning) as excinfo:
-        meta_builder._check_inputs()
-    os.chdir(cwd)
+    with set_wd(self.nfcore_modules):
+        meta_builder = nf_core.modules.ModulesTest("none", True, "")
+        with pytest.raises(UserWarning) as excinfo:
+            meta_builder._check_inputs()
     assert "Cannot find directory" in str(excinfo.value)
 
 
 def test_modules_test_no_name_no_prompts(self):
     """Test the check_inputs() function - raise UserWarning prompts are deactivated and module name is not provided."""
-    cwd = os.getcwd()
-    os.chdir(self.nfcore_modules)
-    meta_builder = nf_core.modules.ModulesTest(None, True, "")
-    with pytest.raises(UserWarning) as excinfo:
-        meta_builder._check_inputs()
-    os.chdir(cwd)
+    with set_wd(self.nfcore_modules):
+        meta_builder = nf_core.modules.ModulesTest(None, True, "")
+        with pytest.raises(UserWarning) as excinfo:
+            meta_builder._check_inputs()
     assert "Tool name not provided and prompts deactivated." in str(excinfo.value)
 
 
 def test_modules_test_no_installed_modules(self):
     """Test the check_inputs() function - raise UserWarning because installed modules were not found"""
-    cwd = os.getcwd()
-    os.chdir(self.nfcore_modules)
-    module_dir = Path(self.nfcore_modules, "modules")
-    shutil.rmtree(module_dir)
-    module_dir.mkdir()
-    meta_builder = nf_core.modules.ModulesTest(None, False, "")
-    meta_builder.repo_type = "modules"
-    with pytest.raises(UserWarning) as excinfo:
-        meta_builder._check_inputs()
-    os.chdir(cwd)
+    with set_wd(self.nfcore_modules):
+        module_dir = Path(self.nfcore_modules, "modules")
+        shutil.rmtree(module_dir)
+        module_dir.mkdir()
+        meta_builder = nf_core.modules.ModulesTest(None, False, "")
+        meta_builder.repo_type = "modules"
+        with pytest.raises(UserWarning) as excinfo:
+            meta_builder._check_inputs()
     assert "No installed modules were found" in str(excinfo.value)

tests/test_test_utils.py

@@ -0,0 +1,50 @@
+import tempfile
+from pathlib import Path
+
+import pytest
+
+from .utils import set_wd, with_temporary_file, with_temporary_folder
+
+
+def test_with_temporary_file():
+    @with_temporary_file
+    def tmp_file_exists(tmp_file):
+        assert Path(tmp_file.name).exists()
+
+    tmp_file_exists()
+
+
+def test_does_not_exist_after():
+    tmp_file = with_temporary_file(lambda x: x.name)()
+    assert not Path(tmp_file).exists()
+
+
+def test_with_temporary_folder():
+    @with_temporary_folder
+    def tmp_folder_exists(tmp_folder):
+        assert Path(tmp_folder).exists()
+
+    tmp_folder_exists()
+
+
+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/utils.py

@@ -5,7 +5,10 @@
 """
 
 import functools
+import os
 import tempfile
+from contextlib import contextmanager
+from pathlib import Path
 
 OLD_TRIMGALORE_SHA = "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
 GITLAB_URL = "https://gitlab.com/nf-core/modules-test.git"
@@ -44,3 +47,21 @@ def wrapper(*args, **kwargs):
             return func(*args, tmpfile, **kwargs)
 
     return wrapper
+
+
+@contextmanager
+def set_wd(path: Path):
+    """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)
+    try:
+        yield
+    finally:
+        os.chdir(start_wd)