Use a context to temporarily change the working directory

CHANGELOG.md

@@ -12,6 +12,7 @@
 ### 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)