Move environment option into build stanza and document it

[bfirsh]

Summary

• Moves the environment cog.yaml option from the top level into the build: stanza, since it's a build-time setting that adds env vars to the Docker image
• Adds documentation for environment in docs/yaml.md
• Maintains backward compatibility: top-level environment still works but emits a deprecation warning

Changes

Config structs: Environment and parsedEnvironment moved from Config to Build. The canonical location is now build.environment.

Backward compatibility: A new resolveEnvironment() validation step handles migration:

• Top-level only → migrated into build.environment with a deprecation warning
• build.environment only → no-op
• Both set → validation error

JSON schema: environment added to build properties; top-level kept with deprecation note.

Documentation: New ### environment section under ## build in docs/yaml.md (alphabetically between cuda and gpu). Documents the NAME=value format, provides an example, and notes reserved variable names.

Tests: Integration test and YAML overwrite test fixtures updated to use the new location.

Example

# New (preferred)
build:
  python_version: "3.12"
  environment:
    - NAME=michael
    - TEST_VAR=test_value

# Old (still works, emits deprecation warning)
build:
  python_version: "3.12"
environment:
  - NAME=michael
  - TEST_VAR=test_value

[ask-bonk]

LGTM

github run

[ask-bonk]

I'm Bonk, and I've done a quick review of your PR.

Moves environment from top-level to build stanza with backward-compatibility migration and deprecation warnings.

Issues:

1. Missing unit tests for backward-compatibility logic (high) — The new resolveEnvironment() function in validate.go has three branches (top-level only → warning, both set → error, build-only → no-op), but none are covered by unit tests. The validate_test.go file should have tests verifying each of these behaviors, similar to the existing TestValidateConfigFileRunPredictCompatibility tests.

2. Missing unit tests for configFileToConfig() environment migration (medium) — parse.go now migrates top-level environment into Build.Environment during parsing (for the FromYAML() path which skips validation). There are no tests verifying this migration works correctly. A test in config_test.go should verify that FromYAML() with top-level environment correctly populates config.Build.Environment.

[ask-bonk]

I'm Bonk, and I've done a quick review of your PR.

Moves environment from top-level to build stanza with backward-compatibility migration and deprecation warnings.

Issues:

1. Missing unit tests for backward-compatibility logic (high) — The new resolveEnvironment() function in validate.go has three branches (top-level only → warning, both set → error, build-only → no-op), but none are covered by unit tests. The validate_test.go file should have tests verifying each of these behaviors, similar to the existing TestValidateConfigFileRunPredictCompatibility tests.

2. Missing unit tests for configFileToConfig() environment migration (medium) — parse.go now migrates top-level environment into Build.Environment during parsing (for the FromYAML() path which skips validation). There are no tests verifying this migration works correctly. A test in config_test.go should verify that FromYAML() with top-level environment correctly populates config.Build.Environment.

github run