junifer 0.0.7.dev332__py3-none-any.whl → 0.0.8__py3-none-any.whl

junifer/cli/tests/test_parser.py

@@ -1,280 +0,0 @@
-"""Provide tests for CLI parser."""
-
-# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
-#          Synchon Mandal <s.mandal@fz-juelich.de>
-# License: AGPL
-
-import sys
-from pathlib import Path
-
-import pytest
-
-from junifer.cli.parser import parse_yaml
-
-
-def test_parse_yaml_failure() -> None:
-    """Test YAML parsing failure."""
-    with pytest.raises(ValueError, match="does not exist"):
-        parse_yaml("foo.yaml")
-
-
-def test_parse_yaml_empty_elements_failure(tmp_path: Path) -> None:
-    """Test YAML parsing with empty elements failure.
-
-    Parameters
-    ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
-
-    """
-    # Write test file
-    fname = tmp_path / "test_parse_yaml_empty_elements_failure.yaml"
-    fname.write_text("elements:")
-    # Check test file
-    with pytest.raises(ValueError, match="elements key was defined"):
-        parse_yaml(fname)
-
-
-def test_parse_yaml_success(tmp_path: Path) -> None:
-    """Test YAML parsing success.
-
-    Parameters
-    ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
-
-    """
-    # Write test file
-    fname = tmp_path / "test_parse_yaml_success.yaml"
-    fname.write_text("foo: bar")
-    # Check test file
-    contents = parse_yaml(fname)
-    assert "foo" in contents
-    assert contents["foo"] == "bar"
-
-
-def test_parse_yaml_success_with_module_autoload(tmp_path: Path) -> None:
-    """Test YAML parsing with single module autoload success.
-
-    Parameters
-    ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
-
-    """
-    # Write test file
-    fname = tmp_path / "test_parse_yaml_with_single_module_autoload.yaml"
-    fname.write_text("foo: bar\nwith: numpy")
-    # Check test file
-    contents = parse_yaml(fname)
-    assert "foo" in contents
-    assert contents["foo"] == "bar"
-    assert "with" in contents
-    assert contents["with"] == ["numpy"]
-    assert "numpy" in sys.modules
-    assert "junifer.configs.wrong_config" not in sys.modules
-
-
-def test_parse_yaml_failure_with_multi_module_autoload(tmp_path: Path) -> None:
-    """Test YAML parsing with multi module autoload failure.
-
-    Parameters
-    ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
-
-    """
-    # Write test file
-    fname = tmp_path / "test_parse_yaml_with_multi_module_autoload.yaml"
-    fname.write_text(
-        "foo: bar\nwith:\n  - numpy\n  - junifer.testing.wrong_config"
-    )
-    # Check test file
-    with pytest.raises(ImportError, match="wrong_config"):
-        parse_yaml(fname)
-
-
-def test_parse_yaml_with_wrong_path(tmp_path: Path) -> None:
-    """Test YAML parsing with wrong paths in with.
-
-    Parameters
-    ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
-
-    """
-    t_tmp_path = tmp_path / "test_relative_with"
-    # Write yaml that includes a relative path
-    yaml_path = t_tmp_path / "yamls"
-    yaml_path.mkdir(exist_ok=True, parents=True)
-    yaml_fname = yaml_path / "test_parse_yaml_wrong_path.yaml"
-
-    yaml_fname.write_text("foo: bar\nwith:\n  -  missingt.py\n  - scipy\n")
-
-    # Check test file
-    with pytest.raises(ValueError, match="does not exist"):
-        parse_yaml(yaml_fname)
-
-
-def test_parse_yaml_relative_path(tmp_path: Path) -> None:
-    """Test YAML parsing with relative paths in with.
-
-    Parameters
-    ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
-
-    """
-    t_tmp_path = tmp_path / "test_relative_with"
-
-    # Write .py to include
-    py_path = t_tmp_path / "external"
-    py_path.mkdir(exist_ok=True, parents=True)
-    py_fname = py_path / "first.py"
-    py_fname.write_text("import numpy as np\n")
-
-    # Write yaml that includes a relative path
-    yaml_path = t_tmp_path / "yamls"
-    yaml_path.mkdir(exist_ok=True, parents=True)
-    yaml_fname = yaml_path / "test_parse_yaml_relative_path.yaml"
-
-    yaml_fname.write_text(
-        "foo: bar\nwith:\n  - ../external/first.py\n  - scipy\n"
-    )
-
-    # Check test file
-    parse_yaml(yaml_fname)
-
-
-def test_parse_yaml_absolute_path(tmp_path: Path) -> None:
-    """Test YAML parsing with absolute paths in with.
-
-    Parameters
-    ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
-
-    """
-    t_tmp_path = tmp_path / "test_relative_with"
-
-    # Write .py to include
-    py_path = t_tmp_path / "external"
-    py_path.mkdir(exist_ok=True, parents=True)
-    py_fname = py_path / "first.py"
-    py_fname.write_text("import numpy as np\n")
-
-    # Write yaml that includes a relative path
-    yaml_path = t_tmp_path / "yamls"
-    yaml_path.mkdir(exist_ok=True, parents=True)
-    yaml_fname = yaml_path / "test_parse_yaml_relative_path.yaml"
-
-    yaml_fname.write_text(
-        f"foo: bar\nwith:\n  - {py_fname.absolute()}\n  - scipy\n"
-    )
-
-    # Check test file
-    parse_yaml(yaml_fname)
-
-
-def test_parse_yaml_multi_module_deps(tmp_path: Path) -> None:
-    """Test YAML parsing with multi-module import with deps.
-
-    Parameters
-    ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
-
-    """
-    t_tmp_path = tmp_path / "test_with_multi_module"
-
-    # Write .py to include
-    py_path = t_tmp_path / "external"
-    py_path.mkdir(exist_ok=True, parents=True)
-    py_fname_1 = py_path / "first.py"
-    py_fname_1.write_text(
-        "import numpy as np\nfrom second import hej\n"
-        "def junifer_module_deps(): return ['second.py']\n"
-    )
-    py_fname_2 = py_path / "second.py"
-    py_fname_2.write_text("def hej(): print('hej')\n")
-
-    # Write yaml
-    yaml_path = t_tmp_path / "yamls"
-    yaml_path.mkdir(exist_ok=True, parents=True)
-    yaml_fname = yaml_path / "test_parse_yaml_multi_module.yaml"
-
-    yaml_fname.write_text(
-        "foo: bar\nwith:\n  - ../external/first.py\n  - scipy\n"
-    )
-
-    # Check test file
-    parse_yaml(yaml_fname)
-
-
-def test_parse_storage_uri_relative(tmp_path: Path) -> None:
-    """Test YAML parsing with storage and relative URI.
-
-    Parameters
-    ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
-
-    """
-    fname = tmp_path / "test_parse_yaml_with_storage_uri.yaml"
-    fname.write_text("foo: bar\nwith: numpy\nstorage:\n  uri: test.db\n")
-
-    contents = parse_yaml(fname)
-    assert "foo" in contents
-    assert contents["foo"] == "bar"
-    assert "storage" in contents
-    assert "uri" in contents["storage"]
-    assert contents["storage"]["uri"] == str(tmp_path / "test.db")
-
-    fname = tmp_path / "test_parse_yaml_with_storage_uri.yaml"
-    fname.write_text(
-        "foo: bar\nwith: numpy\nstorage:\n  uri: ../another/test.db\n"
-    )
-
-    contents = parse_yaml(fname)
-    assert "foo" in contents
-    assert contents["foo"] == "bar"
-    assert "storage" in contents
-    assert "uri" in contents["storage"]
-    assert contents["storage"]["uri"] == str(
-        (tmp_path / "../another/test.db").resolve()
-    )
-
-    fname = tmp_path / "test_parse_yaml_with_storage_uri.yaml"
-    fname.write_text(
-        "foo: bar\nwith: numpy\nstorage:\n  uri: /absolute/test.db\n"
-    )
-
-    contents = parse_yaml(fname)
-    assert "foo" in contents
-    assert contents["foo"] == "bar"
-    assert "storage" in contents
-    assert "uri" in contents["storage"]
-    assert contents["storage"]["uri"] == "/absolute/test.db"
-
-    # Just to trick coverage
-    fname = tmp_path / "test_parse_yaml_with_storage_uri.yaml"
-    fname.write_text("foo: bar\nwith: numpy\nstorage:\n  kind: SomeStorage\n")
-
-    contents = parse_yaml(fname)
-    assert "foo" in contents
-    assert contents["foo"] == "bar"
-    assert "storage" in contents
-
-
-def test_parse_yaml_queue_venv_relative(tmp_path: Path) -> None:
-    """Test YAML parsing with relative venv queue.
-
-    Parameters
-    ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
-
-    """
-    fname = tmp_path / "test_parse_yaml_queue_venv_relative.yaml"
-    fname.write_text("queue:\n  env:\n    kind: venv\n    name: .venv\n")
-    _ = parse_yaml(fname)

junifer/external/h5io/h5io/__init__.py

@@ -1,15 +0,0 @@
-"""Python Objects Onto HDF5
-"""
-
-
-from ._h5io import (
-    has_hdf5,  # noqa, analysis:ignore
-    read_hdf5,  # noqa, analysis:ignore
-    write_hdf5,  # noqa, analysis:ignore
-    _TempDir,  # noqa, analysis:ignore
-    object_diff,  # noqa, analysis:ignore
-    list_file_contents,  # noqa, analysis:ignore
-)
-from ._version import __version__
-from .chunked_array import ChunkedArray  # noqa, analysis:ignore
-from .chunked_list import ChunkedList  # noqa, analysis:ignore