Gh safestore keyerror test

.gitignore

@@ -1,16 +1,24 @@
-.idea
-.vscode
-__pycache__
-.mypy_cache
-*.pyc
-dist
+
+# IDE and editor folders
+.idea/
+.vscode/
+
+# Python cache and environment folders
+venv/
 .venv/
+__pycache__/
+.mypy_cache/
+*.pyc
+.env
+
+# Build and test outputs
+dist/
 .coverage
 coverage.xml
 .ipynb_checkpoints/
-gcs_cache
-results_cache
-tests/anoph/fixture/simulated
+gcs_cache/
+results_cache/
+tests/anoph/fixture/simulated/
 
 # emacs
 *~

tests/test_util_safestore.py

@@ -0,0 +1,62 @@
+import pytest
+from malariagen_data.util import SafeStore
+
+
+def test_safestore_getitem_success():
+    store = {"foo": "bar"}
+    safe_store = SafeStore(store)
+    assert safe_store["foo"] == "bar"
+
+
+def test_safestore_getitem_keyerror_raises_filenotfounderror():
+    store = {}
+    safe_store = SafeStore(store)
+    with pytest.raises(FileNotFoundError) as excinfo:
+        _ = safe_store["missing_key"]
+    # Ensure the missing key is represented in the error message
+    assert "missing_key" in str(excinfo.value)
+    # Ensure the original KeyError is preserved as the cause
+    assert isinstance(excinfo.value.__cause__, KeyError)
+
+
+def test_safestore_len():
+    store = {"a": 1, "b": 2}
+    safe_store = SafeStore(store)
+    assert len(safe_store) == 2
+
+
+def test_safestore_iter():
+    store = {"a": 1, "b": 2}
+    safe_store = SafeStore(store)
+    assert set(iter(safe_store)) == {"a", "b"}
+
+
+def test_safestore_getattr_passthrough():
+    class MockStore:
+        def __init__(self):
+            self.attr = "value"
+
+    store = MockStore()
+    safe_store = SafeStore(store)
+    assert safe_store.attr == "value"
+
+
+def test_safestore_getattr_setstate_raises_attributeerror():
+    store = {}
+    safe_store = SafeStore(store)
+    with pytest.raises(AttributeError):
+        _ = safe_store.__setstate__
+
+
+def test_safestore_setitem_raises_notimplemented():
+    store = {}
+    safe_store = SafeStore(store)
+    with pytest.raises(NotImplementedError):
+        safe_store["foo"] = "bar"
+
+
+def test_safestore_delitem_raises_notimplemented():
+    store = {"foo": "bar"}
+    safe_store = SafeStore(store)
+    with pytest.raises(NotImplementedError):
+        del safe_store["foo"]

venv/Lib/site-packages/_distutils_hack/__init__.py

@@ -0,0 +1,222 @@
+# don't import any costly modules
+import sys
+import os
+
+
+is_pypy = '__pypy__' in sys.builtin_module_names
+
+
+def warn_distutils_present():
+    if 'distutils' not in sys.modules:
+        return
+    if is_pypy and sys.version_info < (3, 7):
+        # PyPy for 3.6 unconditionally imports distutils, so bypass the warning
+        # https://foss.heptapod.net/pypy/pypy/-/blob/be829135bc0d758997b3566062999ee8b23872b4/lib-python/3/site.py#L250
+        return
+    import warnings
+
+    warnings.warn(
+        "Distutils was imported before Setuptools, but importing Setuptools "
+        "also replaces the `distutils` module in `sys.modules`. This may lead "
+        "to undesirable behaviors or errors. To avoid these issues, avoid "
+        "using distutils directly, ensure that setuptools is installed in the "
+        "traditional way (e.g. not an editable install), and/or make sure "
+        "that setuptools is always imported before distutils."
+    )
+
+
+def clear_distutils():
+    if 'distutils' not in sys.modules:
+        return
+    import warnings
+
+    warnings.warn("Setuptools is replacing distutils.")
+    mods = [
+        name
+        for name in sys.modules
+        if name == "distutils" or name.startswith("distutils.")
+    ]
+    for name in mods:
+        del sys.modules[name]
+
+
+def enabled():
+    """
+    Allow selection of distutils by environment variable.
+    """
+    which = os.environ.get('SETUPTOOLS_USE_DISTUTILS', 'local')
+    return which == 'local'
+
+
+def ensure_local_distutils():
+    import importlib
+
+    clear_distutils()
+
+    # With the DistutilsMetaFinder in place,
+    # perform an import to cause distutils to be
+    # loaded from setuptools._distutils. Ref #2906.
+    with shim():
+        importlib.import_module('distutils')
+
+    # check that submodules load as expected
+    core = importlib.import_module('distutils.core')
+    assert '_distutils' in core.__file__, core.__file__
+    assert 'setuptools._distutils.log' not in sys.modules
+
+
+def do_override():
+    """
+    Ensure that the local copy of distutils is preferred over stdlib.
+
+    See https://github.com/pypa/setuptools/issues/417#issuecomment-392298401
+    for more motivation.
+    """
+    if enabled():
+        warn_distutils_present()
+        ensure_local_distutils()
+
+
+class _TrivialRe:
+    def __init__(self, *patterns):
+        self._patterns = patterns
+
+    def match(self, string):
+        return all(pat in string for pat in self._patterns)
+
+
+class DistutilsMetaFinder:
+    def find_spec(self, fullname, path, target=None):
+        # optimization: only consider top level modules and those
+        # found in the CPython test suite.
+        if path is not None and not fullname.startswith('test.'):
+            return
+
+        method_name = 'spec_for_{fullname}'.format(**locals())
+        method = getattr(self, method_name, lambda: None)
+        return method()
+
+    def spec_for_distutils(self):
+        if self.is_cpython():
+            return
+
+        import importlib
+        import importlib.abc
+        import importlib.util
+
+        try:
+            mod = importlib.import_module('setuptools._distutils')
+        except Exception:
+            # There are a couple of cases where setuptools._distutils
+            # may not be present:
+            # - An older Setuptools without a local distutils is
+            #   taking precedence. Ref #2957.
+            # - Path manipulation during sitecustomize removes
+            #   setuptools from the path but only after the hook
+            #   has been loaded. Ref #2980.
+            # In either case, fall back to stdlib behavior.
+            return
+
+        class DistutilsLoader(importlib.abc.Loader):
+            def create_module(self, spec):
+                mod.__name__ = 'distutils'
+                return mod
+
+            def exec_module(self, module):
+                pass
+
+        return importlib.util.spec_from_loader(
+            'distutils', DistutilsLoader(), origin=mod.__file__
+        )
+
+    @staticmethod
+    def is_cpython():
+        """
+        Suppress supplying distutils for CPython (build and tests).
+        Ref #2965 and #3007.
+        """
+        return os.path.isfile('pybuilddir.txt')
+
+    def spec_for_pip(self):
+        """
+        Ensure stdlib distutils when running under pip.
+        See pypa/pip#8761 for rationale.
+        """
+        if self.pip_imported_during_build():
+            return
+        clear_distutils()
+        self.spec_for_distutils = lambda: None
+
+    @classmethod
+    def pip_imported_during_build(cls):
+        """
+        Detect if pip is being imported in a build script. Ref #2355.
+        """
+        import traceback
+
+        return any(
+            cls.frame_file_is_setup(frame) for frame, line in traceback.walk_stack(None)
+        )
+
+    @staticmethod
+    def frame_file_is_setup(frame):
+        """
+        Return True if the indicated frame suggests a setup.py file.
+        """
+        # some frames may not have __file__ (#2940)
+        return frame.f_globals.get('__file__', '').endswith('setup.py')
+
+    def spec_for_sensitive_tests(self):
+        """
+        Ensure stdlib distutils when running select tests under CPython.
+
+        python/cpython#91169
+        """
+        clear_distutils()
+        self.spec_for_distutils = lambda: None
+
+    sensitive_tests = (
+        [
+            'test.test_distutils',
+            'test.test_peg_generator',
+            'test.test_importlib',
+        ]
+        if sys.version_info < (3, 10)
+        else [
+            'test.test_distutils',
+        ]
+    )
+
+
+for name in DistutilsMetaFinder.sensitive_tests:
+    setattr(
+        DistutilsMetaFinder,
+        f'spec_for_{name}',
+        DistutilsMetaFinder.spec_for_sensitive_tests,
+    )
+
+
+DISTUTILS_FINDER = DistutilsMetaFinder()
+
+
+def add_shim():
+    DISTUTILS_FINDER in sys.meta_path or insert_shim()
+
+
+class shim:
+    def __enter__(self):
+        insert_shim()
+
+    def __exit__(self, exc, value, tb):
+        remove_shim()
+
+
+def insert_shim():
+    sys.meta_path.insert(0, DISTUTILS_FINDER)
+
+
+def remove_shim():
+    try:
+        sys.meta_path.remove(DISTUTILS_FINDER)
+    except ValueError:
+        pass

venv/Lib/site-packages/_distutils_hack/override.py

@@ -0,0 +1 @@
+__import__('_distutils_hack').do_override()

venv/Lib/site-packages/distutils-precedence.pth

@@ -0,0 +1 @@
+import os; var = 'SETUPTOOLS_USE_DISTUTILS'; enabled = os.environ.get(var, 'local') == 'local'; enabled and __import__('_distutils_hack').add_shim();

venv/Lib/site-packages/pip-22.3.1.dist-info/INSTALLER

@@ -0,0 +1 @@
+pip

venv/Lib/site-packages/pip-22.3.1.dist-info/LICENSE.txt

@@ -0,0 +1,20 @@
+Copyright (c) 2008-present The pip developers (see AUTHORS.txt file)
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.