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

- 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)

soapy1

Looking great! Just a few UX type questions.

.github/workflows/tests.yml

conda_self/health_checks/base_protection.py

conda_self/plugin.py

conda_self/health_checks/base_protection.py

No need to unlink packages individually from an environment that is about to be deleted entirely.

Previously the check returned silently, making it unclear whether it ran at all. Now prints a clear skip message.

These attributes cannot be passed via conda doctor; simplify to direct constants.

Conda's QuietSpinner still prints "Preparing/Verifying/Executing transaction: ...working... done" lines. Redirect stdout during clone_env and reset calls to fully silence output in quiet mode.

Replace print_explicit with Environment.from_prefix() and the YAML environment exporter plugin, which captures both conda and pip-installed packages in the snapshot.

# Conflicts: # pixi.lock

recipe/meta.yaml

pyproject.toml

conda 26.1.1 has not been released yet; the >=26.1.1 constraint was unsolvable on conda-forge.

soapy1

Looks great! I think if this diff is applied then it should make the package builds work. I think it's ok to be depending on the main channel here.

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 6a3bcc1..3c92488 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -53,7 +53,7 @@ jobs:
           environments: ${{ env.PIXI_ENV_NAME }}
 
       - name: Build recipe
-        run: pixi run --environment ${{ env.PIXI_ENV_NAME }} build --channel conda-forge
+        run: pixi run --environment ${{ env.PIXI_ENV_NAME }} build --channel conda-forge --channel main
 
       - name: Upload to conda-canary
         # Only publish canary builds after successful pushes to main in the canonical repo

marcoesters · 2026-03-05T19:44:39Z

conda_self/health_checks/base_protection.py

+            verbose=False,
+            quiet=True,
+        )
+        reset(uninstallable_packages=uninstallable_packages)


This will keep pip-installed packages in the new protected base environment still, doesn't it? This essentially re-implements conda self migrate, but as a conda doctor fix. Should there be some kind of warning if we encounter non-conda packages?

marcoesters · 2026-03-05T19:47:55Z

conda_self/health_checks/base_protection.py

+        frozen_path.write_text(json.dumps({"message": message}) if message else "")
+    except OSError as e:
+        raise CondaOSError(f"Could not protect environment: {e}") from e
+


I think it would be nice to add an @EXPLICIT file to enable resetting to the post-migration state. Similar to what was done here: marcoesters@c03fd8f#diff-ab450c1dd96dee7dffda61f8532a2e4b44c1f3b3adbcb5f0fd9c3aae8c76dca5R152-R157

marcoesters · 2026-03-05T19:49:51Z

conda_self/health_checks/base_protection.py

@@ -0,0 +1,148 @@
+# Copyright (C) 2012 Anaconda, Inc


Are these (seemingly old) copyright notices needed?

This is consistent with the copyright in conda. Though it doesn't look like any other file in conda-self includes these.

marcoesters · 2026-03-05T19:58:15Z

tests/test_health_check_base_protection.py

+    # Additional fields only available in conda >= 26.1.0
+    if hasattr(hc, "fixer"):


Isn't that always the case since we require conda >= 26.1.0?

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

jezdez added 2 commits February 4, 2026 14:52

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

soapy1 reviewed Feb 12, 2026

View reviewed changes

danyeaw removed this from conda Roadmap and Sprint Planning Feb 17, 2026

jezdez added 8 commits February 26, 2026 11:54

Remove redundant reset() before rm_rf when recreating environment

35cd8b6

No need to unlink packages individually from an environment that is about to be deleted entirely.

Clarify health check summary to explain what 'protected' means

2211cb2

Show skip message when health check runs on non-base environment

d75c018

Previously the check returned silently, making it unclear whether it ran at all. Now prints a clear skip message.

Remove unreachable getattr(args, ...) for default_env and message

3267f3f

These attributes cannot be passed via conda doctor; simplify to direct constants.

Suppress transaction spinner output when --quiet is used

9038871

Conda's QuietSpinner still prints "Preparing/Verifying/Executing transaction: ...working... done" lines. Redirect stdout during clone_env and reset calls to fully silence output in quiet mode.

Add TODO noting explicit format doesn't capture pip packages

d19a10c

Use environment exporter plugin for snapshots

c58edc6

Replace print_explicit with Environment.from_prefix() and the YAML environment exporter plugin, which captures both conda and pip-installed packages in the snapshot.

Merge remote-tracking branch 'origin/main' into fix-base-task

ffbd29d

# Conflicts: # pixi.lock

jezdez requested review from jaimergp and soapy1 February 26, 2026 11:10

jezdez commented Feb 26, 2026

View reviewed changes

recipe/meta.yaml Outdated Show resolved Hide resolved

Apply suggestion from @jezdez

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jezdez commented Feb 26, 2026

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pyproject.toml Show resolved Hide resolved

jezdez commented Feb 26, 2026

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jezdez added 2 commits February 26, 2026 12:13

Apply suggestions from code review

c5a4d53

Revert conda version to >=26.1.0 and update pixi.lock

271d898

conda 26.1.1 has not been released yet; the >=26.1.1 constraint was unsolvable on conda-forge.

soapy1 reviewed Mar 4, 2026

View reviewed changes

jezdez added 2 commits March 5, 2026 14:16

Merge branch 'main' into fix-base-task

bb14151

Add main channel to build recipe command

b5f3269

jezdez requested review from marcoesters and soapy1 March 5, 2026 13:57

marcoesters reviewed Mar 5, 2026

View reviewed changes

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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 63 commits intomainfrom
fix-base-task

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		# Additional fields only available in conda >= 26.1.0
		if hasattr(hc, "fixer"):

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