Register base-protection health check for `conda doctor --fix` by jezdez · Pull Request #88 · conda-incubator/conda-self

jezdez · 2025-12-17T12:15:55Z

Registers a base-protection health check that integrates with conda doctor.

Fixes #74.

Requires: conda >= 26.1.0 (health check fixer API from conda/conda#15530)

What it does

conda doctor - shows if base environment is protected or not
conda doctor --fix - offers to protect your base environment

When fixing, the health check:

Clones your base environment to a new default environment
Resets base to essentials only
Freezes base to prevent accidental modifications
Sets the default activation environment to the new default

Usage

# Check base protection status
conda doctor

# Run fix to protect base environment
conda doctor --fix

# Run only this specific check
conda doctor base-protection
conda doctor base-protection --fix

Changes

Registers base-protection health check via conda_health_checks hook
Health check reports protection status in conda doctor output
Fix capability handles the full protection workflow
Updated README with new CLI syntax
Bumped minimum conda version to 26.1.0

…elp text Fix #74. - Introduced `conda migrate base` for base environment migration. - Added `--list` option to display available migration tasks. - Updated documentation and README to reflect new command structure. - Enhanced tests for new functionality and help commands.

- Remove standalone 'conda migrate' subcommand - Expose base environment protection via 'conda fix base' using conda's new fix task plugin framework - Rename main_migrate.py to main_fix_base.py and clean up unused code - Update README to document both 'conda self' and 'conda fix base' - Update tests to use 'conda fix' instead of 'conda migrate' - Improve test coverage and type hints The 'conda self' subcommand for managing base environment packages remains unchanged. The base protection task is now accessed via 'conda fix base' which uses conda's plugin-based fix task system.

- Update plugin.py: CondaFixTask -> CondaHealthFix - Update plugin.py: conda_fix_tasks -> conda_health_fixes - Update main_fix_base.py docstrings - Update README.md terminology - Update tests for new UI text and error handling - Rename news file This aligns with the conda plugin API rename for better symmetry with 'health checks' from conda doctor.

The CondaHealthFix type only exists in conda versions with the fix subcommand. Wrap the import in try/except so conda-self works with older conda versions (just without the fix base feature).

The base environment protection functionality remains available via conda self commands. The conda_health_fixes hook has been removed from conda in favor of the simpler conda doctor --fix approach.

Register a health check with conda doctor that: - Checks if the base environment is protected (frozen) - Offers to fix by protecting the base environment The health check only runs when checking the base environment and provides verbose output explaining why protection is recommended. Implementation split: hookimpl in plugin.py, functions in health_check.py

Import health check status marks from conda instead of defining locally.

- Move health_check.py to health_checks/base_protection.py - Add health_checks/__init__.py with plugins list - Move @hookimpl decorator into base_protection module - Update plugin.py to import health_checks for registration

Keep the implementation in health_checks/base_protection.py but define the hookimpl in plugin.py with a lazy import to avoid import-time side effects.

- Keep main_fix_base.py as internal implementation for health check fix - Update README to document using 'conda doctor --fix' for base protection - Remove protect subcommand registration that was never completed

- Delete main_fix_base.py - Move all protection workflow logic into health_checks/base_protection.py - The fix is now self-contained in the health check module

- Fix SUCCESS_MESSAGE to show activation command instead of claiming auto-activation - Simplify variable names and reduce redundancy - Shorten warning messages - Use pathlib.Path for cleaner path handling

- Set id='base-protection' for cleaner CLI usage - Update README with new --list and --fix id syntax

- Update CondaHealthCheck to use `fixer` parameter with ConfirmCallback - Replace confirm_yn() calls with confirm() callback passed by framework - Add separate `fix` description parameter for --list output - Bump conda dependency to >=26.1.0 - Add conda-canary channel testing to CI to catch compatibility issues early

The new health check API is on conda main but not released. Keep the existing version requirement for stable channels and test with conda-canary for the unreleased API.

The new health check API (fixer with ConfirmCallback) is only available in conda-canary builds. Only run tests with conda-canary until the required conda version is released. The full test matrix is preserved in comments for easy restoration.

conda-canary may not have Python 3.13 builds for all platforms. Use Python 3.12 and restrict platform solving to linux-64 only.

Pixi tries to solve all environments for all platforms, which fails with conda-canary. Use setup-miniconda directly with conda-canary channel for simpler, more reliable canary testing.

- Test is_base_environment and is_base_protected helper functions - Test check action for base environment detection - Test fix fixer early exit conditions - Test plugin registration (skipped on older conda without fixer API) - Add fallback for OK_MARK/X_MARK constants not in stable conda

- Convert class-based tests to function-based tests - Use pytest fixtures (fake_base_env, protected_base_env) instead of mocks - Use native pytest fixtures (tmp_path, monkeypatch, capsys) - Restructure fix() to defer imports until after confirm callback

The fixer API (with ConfirmCallback) requires conda >= 26.1.0. On older conda versions, only the check action is registered, allowing the plugin to work without the fix functionality.

- Make version assertions more flexible in test_update_all (canary builds have different version string formats) - Skip integration tests (test_reset, test_reset_migrate) for canary builds due to dependency resolution issues with package constraints

- Shorten summary string in plugin.py - Move Path import to TYPE_CHECKING block - Fix line length in test comment

- Use try/except in plugin.py instead of checking __dataclass_fields__ - Use hasattr() in test instead of __dataclass_fields__ - More Pythonic EAFP style

- Skip test_remove_nonessential_plugin (dependency resolution issues) - Skip test_update_all (version mismatch between module and installed)

jezdez · 2026-01-26T13:48:27Z

This is on hold until the conda 26.1.0 release has happened with the require plugin hook.

- Bump conda dependency to >=26.1.0 in pixi config - Restore full test matrix now that health check API is released - Remove backwards compatibility code from plugin.py

jezdez · 2026-02-04T13:47:43Z

Updated for conda 26.1.0 release:

Bumped conda dependency to >=26.1.0
Restored full test matrix (pixi-based)
Simplified plugin.py by removing backwards compatibility code

Ready for review.

- Update inline import comment to explain lazy loading - Remove try/except for OK_MARK/X_MARK (available in conda 26.1.0)

- Change macos-latest to use conda-forge instead of defaults - Remove macOS platforms from pixi config when testing defaults (conda 26.1.0 not available on defaults channel for macOS)

jezdez added 7 commits October 24, 2025 10:09

Merge branch 'main' into migrate-base

d9fbc54

Make health fixes import conditional for older conda versions

4c55b13

The CondaHealthFix type only exists in conda versions with the fix subcommand. Wrap the import in try/except so conda-self works with older conda versions (just without the fix base feature).

Apply pre-commit fixes

032cf79

Move argparse import to TYPE_CHECKING block

a440117

jezdez mentioned this pull request Dec 17, 2025

Refactor conda migrate command to support subcommands and enhance help text #75

Closed

danyeaw added this to conda Roadmap and Sprint Planning Dec 17, 2025

github-project-automation bot moved this to Sorting ⚙️ in conda Roadmap and Sprint Planning Dec 17, 2025

danyeaw moved this from Sorting ⚙️ to In review 🔍 in conda Roadmap and Sprint Planning Dec 17, 2025

danyeaw moved this from In review 🔍 to In Progress 🏗️ in conda Roadmap and Sprint Planning Dec 17, 2025

jezdez added 2 commits December 17, 2025 21:04

Remove health fix API since conda doctor --fix replaces it

52aca94

The base environment protection functionality remains available via conda self commands. The conda_health_fixes hook has been removed from conda in favor of the simpler conda doctor --fix approach.

jezdez force-pushed the fix-base-task branch from 8ee01c5 to 453e283 Compare December 17, 2025 21:40

jezdez added 15 commits December 17, 2025 22:54

Use OK_MARK and X_MARK from conda.base.constants

8e3b67a

Import health check status marks from conda instead of defining locally.

Refactor health check into health_checks module

cdc6a33

- Move health_check.py to health_checks/base_protection.py - Add health_checks/__init__.py with plugins list - Move @hookimpl decorator into base_protection module - Update plugin.py to import health_checks for registration

Move hookimpl back to plugin.py with lazy import

0067648

Keep the implementation in health_checks/base_protection.py but define the hookimpl in plugin.py with a lazy import to avoid import-time side effects.

Remove protect subcommand, use conda doctor --fix instead

489dbac

- Keep main_fix_base.py as internal implementation for health check fix - Update README to document using 'conda doctor --fix' for base protection - Remove protect subcommand registration that was never completed

Consolidate base protection into health check fix

8a9c33d

- Delete main_fix_base.py - Move all protection workflow logic into health_checks/base_protection.py - The fix is now self-contained in the health check module

Clean up base_protection module

fccb4bb

- Fix SUCCESS_MESSAGE to show activation command instead of claiming auto-activation - Simplify variable names and reduce redundancy - Shorten warning messages - Use pathlib.Path for cleaner path handling

Use health check name in frozen file message

c6c4e7b

Simplify health fix output - remove verbose strings

17f9f92

Restore context.quiet checks for progress output

8ae9521

Use set_keys API instead of deprecated _read_rc/_write_rc

df54a22

Show fix suggestion without requiring verbose mode

494f559

Use user_rc_path for default_activation_env setting

dc5f809

Use ConfigurationFile context manager for config updates

b84b071

Remove migrate CLI tests (command removed)

8ffb1ca

Use explicit id for base-protection health check

b160fe6

- Set id='base-protection' for cleaner CLI usage - Update README with new --list and --fix id syntax

Merge branch 'main' into fix-base-task

9d09d0e

danyeaw mentioned this pull request Jan 12, 2026

Add conda doctor --fix for external-packages conda/conda#15582

Open

2 tasks

jezdez marked this pull request as draft January 20, 2026 17:30

jezdez added 15 commits January 26, 2026 13:33

Fix: revert to conda >=25.7.0 since 26.1.0 is not released yet

ed6f98c

The new health check API is on conda main but not released. Keep the existing version requirement for stable channels and test with conda-canary for the unreleased API.

Fix canary test: use Python 3.12 and restrict to linux-64

b49e351

conda-canary may not have Python 3.13 builds for all platforms. Use Python 3.12 and restrict platform solving to linux-64 only.

Use setup-miniconda instead of pixi for canary testing

803593f

Pixi tries to solve all environments for all platforms, which fails with conda-canary. Use setup-miniconda directly with conda-canary channel for simpler, more reliable canary testing.

Fix setup-miniconda action sha

2f7875b

Install conda from canary channel in test environment

c8b74b2

Fix verification: ConfirmCallback is TYPE_CHECKING only

666cc24

Make health check backward compatible with older conda versions

0a4c6b8

The fixer API (with ConfirmCallback) requires conda >= 26.1.0. On older conda versions, only the check action is registered, allowing the plugin to work without the fix functionality.

Fix linting issues

085d5d7

- Shorten summary string in plugin.py - Move Path import to TYPE_CHECKING block - Fix line length in test comment

Use try/except and hasattr for API detection

b8d7ea1

- Use try/except in plugin.py instead of checking __dataclass_fields__ - Use hasattr() in test instead of __dataclass_fields__ - More Pythonic EAFP style

Skip additional integration tests for canary builds

ba21a7f

- Skip test_remove_nonessential_plugin (dependency resolution issues) - Skip test_update_all (version mismatch between module and installed)

Update for conda 26.1.0 release

19a73c7

- Bump conda dependency to >=26.1.0 in pixi config - Restore full test matrix now that health check API is released - Remove backwards compatibility code from plugin.py

jezdez marked this pull request as ready for review February 4, 2026 13:48

jezdez added 4 commits February 4, 2026 14:50

Clean up outdated comments and remove backwards compat code

27a663e

- Update inline import comment to explain lazy loading - Remove try/except for OK_MARK/X_MARK (available in conda 26.1.0)

Bump conda requirement to >=26.1.0 in recipe

339357e

Remove conda-canary skipif decorators from tests

c51a1a5

Update pixi.lock

65201ff

danyeaw moved this from In Progress 🏗️ to In review 🔍 in conda Roadmap and Sprint Planning Feb 4, 2026

danyeaw assigned jezdez Feb 4, 2026

jezdez added 2 commits February 4, 2026 17:47

Fix test matrix: conda not available on defaults for macOS

d1e7518

- Change macos-latest to use conda-forge instead of defaults - Remove macOS platforms from pixi config when testing defaults (conda 26.1.0 not available on defaults channel for macOS)

Fix: only osx-64 lacks conda on defaults, not osx-arm64

f6355e0

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Register base-protection health check for `conda doctor --fix`#88

Register base-protection health check for `conda doctor --fix`#88
jezdez wants to merge 50 commits intomainfrom
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jezdez commented Dec 17, 2025 •

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