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Add option to always keep temporary files (#199)
* Add option to always keep temporary files * Simplify tempcd * Specify type of BEFLOW_KEEP_TMP_FILES * Add tests for temporary_cd * Update temporary_cd to pass tests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix test warnings * Add comment * Support multi-part paths without parents argument * Remove print statements from temporary_cd * Changes to optimizer worker to support KEEP_TMP_FILES * Try to keep QCEngine's scratch files * Deprecate BEFLOW_OPTIMIZER_KEEP_FILES * Revert "Try to keep QCEngine's scratch files" This reverts commit ff8dc2e. * Revert tests to use openff.utilities' temporary_cd * Consolidate various methods of deleting temporary files * Ensure deprecated alias of setting is unset in tests --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,136 @@ | ||
| from pathlib import Path | ||
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| import pytest | ||
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| from openff.bespokefit.utilities.tempcd import temporary_cd | ||
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| @pytest.mark.parametrize( | ||
| "path", | ||
| [ | ||
| "tempcd_test", | ||
| "tempcd/test", | ||
| Path("tempcd_test"), | ||
| None, | ||
| ".", | ||
| "", | ||
| ], | ||
| ) | ||
| class TestTemporaryCD: | ||
| @pytest.fixture(autouse=True) | ||
| def run_test_in_empty_temporary_directory(self, monkeypatch, tmp_path): | ||
| """ | ||
| Tests in this class should run in their own empty temporary directories | ||
| This fixture creates a temporary directory for the test, moves into it, | ||
| and deletes it when the test is finished. | ||
| """ | ||
| monkeypatch.chdir(tmp_path) | ||
|
|
||
| def test_tempcd_changes_dir(self, path): | ||
| """ | ||
| Check temporary_cd changes directory to the target directory | ||
| """ | ||
| # Arrange | ||
| starting_path = Path(".").resolve() | ||
|
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||
| # Act | ||
| with temporary_cd(path): | ||
| temp_path = Path(".").resolve() | ||
|
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| # Assert | ||
| if path is None: | ||
| assert temp_path.parent == starting_path | ||
| else: | ||
| assert temp_path == (starting_path / path).resolve() | ||
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||
| def test_tempcd_changes_back(self, path): | ||
| """ | ||
| Check temporary_cd returns to original directory when context manager exits | ||
| """ | ||
| # Arrange | ||
| starting_path = Path(".").resolve() | ||
|
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||
| # Act | ||
| with temporary_cd(path): | ||
| pass | ||
|
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||
| # Assert | ||
| assert Path(".").resolve() == starting_path | ||
|
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| def test_tempcd_cleans_up_temporary_directory(self, path, monkeypatch): | ||
| """ | ||
| Check temporary_cd cleans up temporary directories it creates when | ||
| BEFLOW_KEEP_TMP_FILES is not set | ||
| This test is skipped when it is parametrized to operate on the working | ||
| directory because the working directory must exist and therefore cannot | ||
| be a temporary directory. This check is hard-coded to check for the | ||
| path being ``"."`` or ``""``, rather than simply checking if the path | ||
| exists, so that conflicts between runs will be detected (though such | ||
| conflicts should be prevented by the | ||
| ``run_test_in_empty_temporary_directory`` fixture) | ||
| """ | ||
| if path in [".", ""]: | ||
| pytest.skip("'Temporary' directory exists") | ||
|
|
||
| # Arrange | ||
| monkeypatch.delenv("BEFLOW_KEEP_TMP_FILES", raising=False) | ||
| monkeypatch.delenv("BEFLOW_OPTIMIZER_KEEP_TMP_FILES", raising=False) | ||
|
|
||
| # Act | ||
| with temporary_cd(path): | ||
| Path("touch").write_text("Ensure cleanup of directories with files") | ||
| temp_path = Path(".").resolve() | ||
|
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| # Assert | ||
| assert not temp_path.exists() | ||
|
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| def test_tempcd_keeps_temporary_directory(self, path, monkeypatch): | ||
| """ | ||
| Check temporary_cd keeps temporary directories it creates when | ||
| BEFLOW_KEEP_TMP_FILES is set | ||
| """ | ||
| # Arrange | ||
| monkeypatch.setenv("BEFLOW_KEEP_TMP_FILES", "1") | ||
| monkeypatch.delenv("BEFLOW_OPTIMIZER_KEEP_TMP_FILES", raising=False) | ||
|
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||
| # Act | ||
| with temporary_cd(path): | ||
| temp_path = Path(".").resolve() | ||
|
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| # Assert | ||
| assert temp_path.exists() | ||
|
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| @pytest.mark.parametrize("keep_tmp_files", [True, False]) | ||
| def test_tempcd_keeps_existing_directory(self, path, monkeypatch, keep_tmp_files): | ||
| """ | ||
| Check temporary_cd keeps existing directories | ||
| This test is skipped when the path is ``None`` because it guarantees | ||
| that the path does not exist. The target directory will be created in | ||
| the Arrange section, unless it is the working directory (in which case | ||
| it already exists). This test is hard-coded to check for the path being | ||
| ``"."`` or ``""``, rather than simply checking if the path exists, so | ||
| that conflicts between runs will be detected (though such conflicts | ||
| should be prevented by the ``run_test_in_empty_temporary_directory`` | ||
| fixture) | ||
| """ | ||
| if path is None: | ||
| pytest.skip("Temporary directory is guaranteed not to exist") | ||
|
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||
| # Arrange | ||
| if path not in [".", ""]: | ||
| Path(path).mkdir(parents=True) | ||
| if keep_tmp_files: | ||
| monkeypatch.setenv("BEFLOW_KEEP_TMP_FILES", "1") | ||
| else: | ||
| monkeypatch.delenv("BEFLOW_KEEP_TMP_FILES", raising=False) | ||
| monkeypatch.delenv("BEFLOW_OPTIMIZER_KEEP_TMP_FILES", raising=False) | ||
|
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||
| # Act | ||
| with temporary_cd(path): | ||
| pass | ||
|
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||
| # Assert | ||
| assert Path(path).is_dir() |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,58 @@ | ||
| """""" | ||
| import os | ||
| import shutil | ||
| import tempfile | ||
| from contextlib import contextmanager | ||
| from pathlib import Path | ||
| from typing import Optional, Union | ||
|
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| from openff.bespokefit.executor.services import current_settings | ||
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| @contextmanager | ||
| def temporary_cd(path: Optional[Union[str, Path]] = None): | ||
| """ | ||
| Context manager to move the current working directory to the path specified. | ||
| If no path is given or the path does not exist, a temporary directory will | ||
| be created. This temporary directory and its contents will be deleted when | ||
| the context manager exits. | ||
| Parameters | ||
| ---------- | ||
| path | ||
| The path to CD into. If ``None`` or not specified, a temporary directory | ||
| will be created. If specified but the path does not exist, a temporary | ||
| directory with that name will be created. | ||
| """ | ||
| # Normalize path to a pathlib Path | ||
| path: Optional[Path] = None if path is None else Path(path) | ||
|
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| # Decide whether to clean up based on bespokefit settings | ||
| settings = current_settings() | ||
| cleanup = not ( | ||
| settings.BEFLOW_OPTIMIZER_KEEP_FILES or settings.BEFLOW_KEEP_TMP_FILES | ||
| ) | ||
|
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| # If a path is not given, create a temporary directory | ||
| if path is None: | ||
| path = Path(tempfile.mkdtemp(dir=".")) | ||
| # If a path is given but does not already exist, create it | ||
| elif not path.exists(): | ||
| path.mkdir(parents=True) | ||
| # If we didn't create the path, do NOT clean it up | ||
| else: | ||
| cleanup = False | ||
|
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| old_directory = os.getcwd() | ||
|
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| try: | ||
| os.chdir(path) | ||
| yield | ||
|
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| finally: | ||
| os.chdir(old_directory) | ||
| # If we created the directory, clean it up | ||
| if cleanup: | ||
| print(f"cleaning up temporary directory {path}") | ||
| shutil.rmtree(path) |