Gh safestore keyerror test by karthik642006 · Pull Request #1243 · malariagen/malariagen-data-python

karthik642006 · 2026-03-29T02:47:52Z

No description provided.

The `SafeStore.__getitem__` method (formerly `ZarrNotFilledStore`) was missing a test for the `KeyError` exception path where it should raise a `FileNotFoundError`. This is important for ensuring that zarr propagates the exception rather than filling. This PR adds: - `tests/test_util_safestore.py`: A new unit test file for the `SafeStore` class. Coverage: - Happy path for `__getitem__`. - `KeyError` path for `__getitem__` (raising `FileNotFoundError`). - `__len__`, `__iter__`, `__getattr__` (passthrough and `__setstate__` restriction). - `__setitem__` and `__delitem__` (raising `NotImplementedError`). The improvement ensures better reliability and coverage for this critical data-access utility.

…247568595985667

Copilot

Pull request overview

This PR’s stated goal is to add unit tests for SafeStore.__getitem__ error translation (KeyError → FileNotFoundError). However, the diff also includes a large number of new files under venv/Lib/site-packages/… (including pip and _distutils_hack), which looks like an accidentally committed virtual environment and does not align with the PR description.

Changes:

Add tests/test_util_safestore.py to cover SafeStore behaviors (including KeyError translation).
Add many files under venv/Lib/site-packages/... (pip internals and dist-info), likely from a local virtualenv (unexpected / unrelated to SafeStore tests).

Reviewed changes

Copilot reviewed 107 out of 756 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
venv/Lib/site-packages/pip/_internal/req/init.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/pyproject.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/operations/install/legacy.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/operations/install/editable_legacy.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/operations/install/init.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/operations/freeze.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/operations/check.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/operations/build/wheel_legacy.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/operations/build/wheel_editable.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/operations/build/wheel.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/operations/build/metadata_legacy.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/operations/build/metadata_editable.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/operations/build/metadata.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/operations/build/build_tracker.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/network/xmlrpc.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/network/utils.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/network/lazy_wheel.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/network/download.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/network/cache.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/network/init.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/models/wheel.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/models/target_python.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/models/selection_prefs.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/models/search_scope.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/models/scheme.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/models/installation_report.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/models/index.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/models/format_control.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/models/direct_url.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/models/candidate.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/models/init.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/metadata/importlib/_envs.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/metadata/importlib/_dists.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/metadata/importlib/_compat.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/metadata/importlib/init.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/metadata/_json.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/metadata/init.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/main.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/locations/base.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/locations/_sysconfig.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/locations/_distutils.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/index/sources.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/index/init.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/distributions/wheel.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/distributions/sdist.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/distributions/installed.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/distributions/base.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/distributions/init.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/commands/wheel.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/commands/uninstall.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/commands/show.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/commands/search.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/commands/inspect.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/commands/index.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/commands/help.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/commands/hash.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/commands/freeze.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/commands/download.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/commands/debug.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/commands/completion.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/commands/check.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/commands/cache.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/commands/init.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/cli/status_codes.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/cli/spinners.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/cli/progress_bars.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/cli/main_parser.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/cli/main.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/cli/command_context.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/cli/base_command.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/cli/autocompletion.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/cli/init.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/_internal/init.py	New pip internal module (unexpected vendored/venv content).
venv/Lib/site-packages/pip/pip-runner.py	New pip file (unexpected vendored/venv content).
venv/Lib/site-packages/pip/main.py	New pip file (unexpected vendored/venv content).
venv/Lib/site-packages/pip/init.py	New pip file (unexpected vendored/venv content).
venv/Lib/site-packages/pip-22.3.1.dist-info/top_level.txt	New dist-info file (unexpected vendored/venv content).
venv/Lib/site-packages/pip-22.3.1.dist-info/entry_points.txt	New dist-info file (unexpected vendored/venv content).
venv/Lib/site-packages/pip-22.3.1.dist-info/WHEEL	New dist-info file (unexpected vendored/venv content).
venv/Lib/site-packages/pip-22.3.1.dist-info/METADATA	New dist-info file (unexpected vendored/venv content).
venv/Lib/site-packages/pip-22.3.1.dist-info/LICENSE.txt	New dist-info file (unexpected vendored/venv content).
venv/Lib/site-packages/pip-22.3.1.dist-info/INSTALLER	New dist-info file (unexpected vendored/venv content).
venv/Lib/site-packages/distutils-precedence.pth	New venv/site-packages file (unexpected).
venv/Lib/site-packages/_distutils_hack/override.py	New venv/site-packages file (unexpected).
venv/Lib/site-packages/_distutils_hack/init.py	New venv/site-packages file (unexpected).
tests/test_util_safestore.py	Adds the intended `SafeStore` unit tests described in the PR.

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Copilot · 2026-03-29T02:49:14Z

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

+from typing import List, Optional
+
+__version__ = "22.3.1"
+
+
+def main(args: Optional[List[str]] = None) -> int:
+    """This is an internal API only meant for use by pip's own console scripts.
+
+    For additional details, see https://github.com/pypa/pip/issues/7498.
+    """
+    from pip._internal.utils.entrypoints import _wrapper
+
+    return _wrapper(args)


The PR description says 'No changes to production code' and that it only adds SafeStore tests, but this diff also introduces a large number of files under venv/Lib/site-packages/... (including pip itself). These appear unrelated to the stated goal and should be removed from the PR so the change set matches the intent.

@copilot apply changes based on this feedback

Copilot · 2026-03-29T02:49:14Z

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();


It looks like a local virtual environment (or its site-packages) was committed into the repository. Committing venv/ content is brittle (OS- and Python-version specific), adds a lot of noise to reviews, and can create confusing runtime behavior. Remove the venv/ directory from version control and add it (and other environment artifacts like .venv/, __pycache__/, *.dist-info/ under venv) to .gitignore.

Suggested change

import os; var = 'SETUPTOOLS_USE_DISTUTILS'; enabled = os.environ.get(var, 'local') == 'local'; enabled and __import__('_distutils_hack').add_shim();

# This file belonged to a local Python virtual environment and should not be committed to version control.

# Recreate your virtual environment locally instead of relying on venv/ content from the repository.

Copilot · 2026-03-29T02:49:14Z

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

+Metadata-Version: 2.1
+Name: pip
+Version: 22.3.1
+Summary: The PyPA recommended tool for installing Python packages.
+Home-page: https://pip.pypa.io/
+Author: The pip developers
+Author-email: distutils-sig@python.org
+License: MIT
+Project-URL: Documentation, https://pip.pypa.io
+Project-URL: Source, https://github.com/pypa/pip
+Project-URL: Changelog, https://pip.pypa.io/en/stable/news/
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Topic :: Software Development :: Build Tools
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Programming Language :: Python :: Implementation :: PyPy
+Requires-Python: >=3.7
+License-File: LICENSE.txt
+
+pip - The Python Package Installer
+==================================
+
+.. image:: https://img.shields.io/pypi/v/pip.svg
+   :target: https://pypi.org/project/pip/
+
+.. image:: https://readthedocs.org/projects/pip/badge/?version=latest
+   :target: https://pip.pypa.io/en/latest
+
+pip is the `package installer`_ for Python. You can use pip to install packages from the `Python Package Index`_ and other indexes.
+
+Please take a look at our documentation for how to install and use pip:
+


Checking dependency artifacts (like *.dist-info metadata) into the repo can significantly inflate repository size and slow down CI, packaging, and developer workflows. It also makes upgrades/downgrades of the environment hard to reason about. These environment-generated files should not be part of this PR/repo unless the project explicitly vendors dependencies (and then they should live outside a venv/ path with a clear vendoring process).

Suggested change

Metadata-Version: 2.1

Name: pip

Version: 22.3.1

Summary: The PyPA recommended tool for installing Python packages.

Home-page: https://pip.pypa.io/

Author: The pip developers

Author-email: distutils-sig@python.org

License: MIT

Project-URL: Documentation, https://pip.pypa.io

Project-URL: Source, https://github.com/pypa/pip

Project-URL: Changelog, https://pip.pypa.io/en/stable/news/

Classifier: Development Status :: 5 - Production/Stable

Classifier: Intended Audience :: Developers

Classifier: License :: OSI Approved :: MIT License

Classifier: Topic :: Software Development :: Build Tools

Classifier: Programming Language :: Python

Classifier: Programming Language :: Python :: 3

Classifier: Programming Language :: Python :: 3 :: Only

Classifier: Programming Language :: Python :: 3.7

Classifier: Programming Language :: Python :: 3.8

Classifier: Programming Language :: Python :: 3.9

Classifier: Programming Language :: Python :: 3.10

Classifier: Programming Language :: Python :: 3.11

Classifier: Programming Language :: Python :: Implementation :: CPython

Classifier: Programming Language :: Python :: Implementation :: PyPy

Requires-Python: >=3.7

License-File: LICENSE.txt

pip - The Python Package Installer

==================================

.. image:: https://img.shields.io/pypi/v/pip.svg

:target: https://pypi.org/project/pip/

.. image:: https://readthedocs.org/projects/pip/badge/?version=latest

:target: https://pip.pypa.io/en/latest

pip is the `package installer`_ for Python. You can use pip to install packages from the `Python Package Index`_ and other indexes.

Please take a look at our documentation for how to install and use pip:

# This file was previously an environment-generated pip METADATA file.

# Dependency artifacts from virtual environments (e.g. venv/Lib/site-packages/*.dist-info)

# should not be committed to version control. The original contents have been

# removed to avoid checking in virtual environment state.

Copilot

Pull request overview

Copilot reviewed 107 out of 757 changed files in this pull request and generated 2 comments.

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Copilot · 2026-03-29T04:14:57Z

venv/Lib/site-packages/pip/_internal/__init__.py

+from typing import List, Optional
+
+import pip._internal.utils.inject_securetransport  # noqa
+from pip._internal.utils import _log
+
+# init_logging() must be called before any call to logging.getLogger()
+# which happens at import of most modules.
+_log.init_logging()
+
+
+def main(args: (Optional[List[str]]) = None) -> int:
+    """This is preserved for old console scripts that may still be referencing
+    it.
+
+    For additional details, see https://github.com/pypa/pip/issues/7498.
+    """
+    from pip._internal.utils.entrypoints import _wrapper
+
+    return _wrapper(args)


The PR description says it only adds SafeStore tests and makes no production changes, but this PR includes a large number of new files under venv/Lib/site-packages/** (including pip internals and dist-info). These look like accidentally committed virtualenv/site-packages contents and will bloat the repo + make reproducible builds harder. Mandatory: remove the committed venv/ directory from the PR and add an ignore rule (e.g., venv/, .venv/, **/site-packages/) so it can’t be reintroduced.

@copilot apply changes based on this feedback

tests/test_util_safestore.py

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Copilot

Pull request overview

Copilot reviewed 107 out of 757 changed files in this pull request and generated 4 comments.

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

Copilot · 2026-03-29T05:18:06Z

venv/Lib/site-packages/pip/_internal/req/__init__.py

+import collections
+import logging
+from typing import Generator, List, Optional, Sequence, Tuple


The PR description says there are no production code changes and only targeted SafeStore tests, but this PR adds a large number of venv/Lib/site-packages/... files (vendored pip and environment artifacts). This is a substantial, unrelated change and will obscure review/CI signals. Mandatory: remove venv/ (and other environment-generated files) from the PR, and add appropriate ignore rules (e.g., venv/, .venv/) to prevent reintroduction.

Copilot · 2026-03-29T05:18:07Z

venv/Lib/site-packages/pip/_internal/network/lazy_wheel.py

+from contextlib import contextmanager
+from tempfile import NamedTemporaryFile
+from typing import Any, Dict, Generator, List, Optional, Tuple
+from zipfile import BadZipfile, ZipFile


If these vendored files are intended to be kept (though they appear accidental), zipfile’s exception is BadZipFile (capital 'F') in modern Python. Importing BadZipfile can fail depending on the runtime/version. Mandatory if keeping this file: switch to importing/handling BadZipFile.

Suggested change

from zipfile import BadZipfile, ZipFile

from zipfile import BadZipFile, ZipFile

tests/test_util_safestore.py

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

karthik642006 and others added 4 commits March 28, 2026 08:05

Merge branch 'malariagen:master' into GH-safestore-keyerror-test-8239…

b26c1dc

…247568595985667

GH-safestore-keyerror-test

2ede146

Merge branch 'malariagen:master' into GH-safestore-keyerror-test

51b4b35

Copilot AI review requested due to automatic review settings March 29, 2026 02:47

Copilot AI reviewed Mar 29, 2026

View reviewed changes

Update .gitignore to ignore unwanted files

b1244a2

karthik642006 requested a review from Copilot March 29, 2026 04:13

Copilot AI reviewed Mar 29, 2026

View reviewed changes

Update tests/test_util_safestore.py

7eb46d7

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

karthik642006 requested a review from Copilot March 29, 2026 05:16

Copilot AI reviewed Mar 29, 2026

View reviewed changes

Update tests/test_util_safestore.py

6703492

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

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

	import os; var = 'SETUPTOOLS_USE_DISTUTILS'; enabled = os.environ.get(var, 'local') == 'local'; enabled and __import__('_distutils_hack').add_shim();
	# This file belonged to a local Python virtual environment and should not be committed to version control.
	# Recreate your virtual environment locally instead of relying on venv/ content from the repository.

	from zipfile import BadZipfile, ZipFile
	from zipfile import BadZipFile, ZipFile

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karthik642006 commented Mar 29, 2026 •

edited

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