Add --restore flag to apply command for clean package restoration by nomyfan · Pull Request #9 · nomyfan/patch-package-py

nomyfan · 2026-05-26T15:34:46Z

Summary

This PR adds a --restore flag to the apply command that allows users to restore a package to its clean state before applying patches. This is useful when the environment may already contain a previous version of the patch or manual edits.

Key Changes

New --restore parameter in apply_patch() function: Added optional env_path and restore parameters to the apply_patch() function. When restore=True, the function calls restore_clean_package() before attempting to apply the patch.
CLI flag support: Added --restore argument to the apply subcommand that passes the flag through to apply_patch().
Validation: Added validation to ensure env_path is provided when restore=True, raising a ValueError if missing.
Improved error handling: Modified error logging to distinguish between:
- "already applied" warnings when restore=False (existing behavior)
- "Failed to apply patch" errors when restore=True and the patch fails after restoration (new behavior)
Documentation updates: Updated SKILL.md to document the new --restore flag and clarified terminology around "restore" vs "reinstall" throughout the documentation.

Implementation Details

The restore operation happens before the dry-run patch check, ensuring the package is in a clean state before validation
The dry-run and actual patch application still occur after restoration (3 subprocess calls total when restore is enabled)
Error messages are context-aware: when a patch fails after restoration, it's logged as an error rather than assuming it was already applied
The --restore flag is optional and defaults to False to maintain backward compatibility

https://claude.ai/code/session_01UUAdSdSQWt6eAP11HMQU3J

…pplying diff https://claude.ai/code/session_01UUAdSdSQWt6eAP11HMQU3J

…-skip-restore https://claude.ai/code/session_01UUAdSdSQWt6eAP11HMQU3J

https://claude.ai/code/session_01UUAdSdSQWt6eAP11HMQU3J

…tore" terminology https://claude.ai/code/session_01UUAdSdSQWt6eAP11HMQU3J

https://claude.ai/code/session_01UUAdSdSQWt6eAP11HMQU3J

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Copilot

Pull request overview

This PR introduces a --restore option for the p12y apply workflow to restore (force-reinstall) a package to a clean state before applying patch files, which helps recover from previously-applied patches or manual edits in the environment.

Changes:

Added --restore flag to the apply subcommand and plumbed it through to core.apply_patch().
Extended apply_patch() with restore/env_path parameters and a call to restore_clean_package() when enabled.
Updated documentation and added unit tests covering the new restore behavior.

Reviewed changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
`patch_package_py/core.py`	Adds restore-aware behavior to `apply_patch()` (including new parameters and error logging).
`patch_package_py/cli.py`	Adds `--restore` CLI flag and passes it into `apply_patch()`.
`skills/patch-package-py/SKILL.md`	Documents `--restore` and updates “reinstall” → “restore” terminology.
`tests/test_core.py`	Adds tests validating restore invocation and related error handling.
`tests/test_e2e.py`	Formatting-only changes (line wrapping).

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…store mode - Move restore_clean_package call before resolve/version checks so --restore can recover a missing or version-drifted package - Raise RuntimeError (non-zero exit) when dry-run fails after restore instead of silently returning https://claude.ai/code/session_01UUAdSdSQWt6eAP11HMQU3J

Copilot

Pull request overview

Copilot reviewed 5 out of 5 changed files in this pull request and generated 3 comments.

        logger.warning(
            f"Patch `{patch_name}` appears to be already applied, skipping...",
        )


When restore=True and the real patch application fails (after a successful dry-run), raise RuntimeError instead of leaking a raw CalledProcessError. Adds test coverage for this scenario. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

The restore happy path test now uses a real venv and real patch command instead of mocking subprocess. Error branch tests (missing env_path, dry-run failure, real apply failure) stay in unit tests since they need to simulate specific failure scenarios. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Copilot

Pull request overview

Copilot reviewed 5 out of 5 changed files in this pull request and generated 2 comments.

Comments suppressed due to low confidence (1)

patch_package_py/core.py:396

Same as above: from None drops the original CalledProcessError context on real apply failures when restore=True, making it harder to debug why patch application failed.

    except subprocess.CalledProcessError:
        if restore:
            raise RuntimeError(
                f"Failed to apply patch `{patch_name}` after restoring clean package."
            ) from None

…n change Previously --restore ran before version validation, which meant it would force-reinstall the version from the patch filename regardless of what the project actually had installed. Now version mismatch is caught first, and restore only reinstalls when the versions already match. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Remove `from None` so the underlying CalledProcessError is chained, making failures easier to diagnose. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

apply_patch now derives site_packages_dir internally via find_site_packages, eliminating the redundant parameter that callers always computed from env_path. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Copilot

Pull request overview

Copilot reviewed 5 out of 5 changed files in this pull request and generated 3 comments.

+        apply_patch(
+            patch_file,
+            env_path,
+            restore=args.restore,
+        )


Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

claude added 5 commits May 26, 2026 15:19

feat(apply): add --reinstall flag to reinstall clean package before a…

48df3af

…pplying diff https://claude.ai/code/session_01UUAdSdSQWt6eAP11HMQU3J

refactor(apply): rename reinstall -> restore to align with commit's -…

c764949

…-skip-restore https://claude.ai/code/session_01UUAdSdSQWt6eAP11HMQU3J

fix: remove unused variable and apply ruff format

e962eab

https://claude.ai/code/session_01UUAdSdSQWt6eAP11HMQU3J

fix(commit): update --skip-restore description to use consistent "res…

4f4aac0

…tore" terminology https://claude.ai/code/session_01UUAdSdSQWt6eAP11HMQU3J

docs(skill): document --restore flag for apply command

fe81350

https://claude.ai/code/session_01UUAdSdSQWt6eAP11HMQU3J

nomyfan requested a review from Copilot May 26, 2026 15:35

Copilot started reviewing on behalf of nomyfan May 26, 2026 15:35 View session

chatgpt-codex-connector Bot reviewed May 26, 2026

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Comment thread patch_package_py/core.py

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Comment thread patch_package_py/core.py

Comment thread patch_package_py/core.py Outdated

nomyfan requested a review from Copilot May 26, 2026 15:44

Copilot started reviewing on behalf of nomyfan May 26, 2026 15:46 View session

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Comment thread patch_package_py/core.py Outdated

Comment thread patch_package_py/core.py

Comment on lines 374 to 376

logger.warning(

f"Patch `{patch_name}` appears to be already applied, skipping...",

)

Comment thread tests/test_core.py Outdated

nomyfan and others added 2 commits May 26, 2026 23:55

nomyfan requested a review from Copilot May 26, 2026 16:03

Copilot started reviewing on behalf of nomyfan May 26, 2026 16:03 View session

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Comment thread patch_package_py/core.py Outdated

Comment thread patch_package_py/core.py Outdated

nomyfan and others added 3 commits May 27, 2026 00:10

fix(apply): preserve exception chain in restore error handling

b685905

Remove `from None` so the underlying CalledProcessError is chained, making failures easier to diagnose. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

refactor(apply): replace redundant site_packages_dir param with env_path

09f48a1

apply_patch now derives site_packages_dir internally via find_site_packages, eliminating the redundant parameter that callers always computed from env_path. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

nomyfan requested a review from Copilot May 30, 2026 02:17

Copilot started reviewing on behalf of nomyfan May 30, 2026 02:17 View session

Copilot AI reviewed May 30, 2026

View reviewed changes

Comment thread patch_package_py/cli.py

Comment on lines +106 to +110

apply_patch(

patch_file,

env_path,

restore=args.restore,

)

Comment thread tests/test_e2e.py Outdated

Comment thread tests/test_e2e.py

fix(test): align terminology from "reinstall" to "restore" in e2e tests

d9a8db1

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

nomyfan merged commit e510a43 into main May 30, 2026
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Add --restore flag to apply command for clean package restoration#9

Add --restore flag to apply command for clean package restoration#9
nomyfan merged 12 commits into
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claude/eager-gates-QTmY1

nomyfan commented May 26, 2026

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nomyfan commented May 26, 2026

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