[leifdenby]

Addresses bullet 5 of my notes on #30: "current cli, runner and verification to the .pipeline submodule".

Changes

• cli.py, runner.py and verification.py move to pipeline/.
• transformations/ moves to pipeline/transformations/, because only the runner uses it.
• utils/config.py, utils/dates.py and utils/save.py move to pipeline/config.py, pipeline/dates.py and pipeline/save.py. These are pipeline-only helpers. utils/ keeps projections and traits, which accessor and alignment use.
• Console script: mxalign = "mxalign.pipeline.cli:main".
• mxalign/__init__.py still re-exports transform, available_transformations and register_transformation. __all__ now lists accessor / alignment / pipeline.
• README.md and examples/advanced.ipynb updated to from mxalign.pipeline.runner import Runner; tests updated to the new paths.

Top level is now accessor, alignment and pipeline, plus utils. The orphaned loaders/ifs_forecast.py, which imports modules that no longer exist, is left alone here.

All 93 tests pass, and mxalign --help works.

🤖 Generated with Claude Code

[Copilot]

🔵 Needs a closer look

It is a package-wide public API/import reorganization stacked on two still-unmerged PRs against a feature branch, which warrants final human confirmation even though the mechanical moves verify as consistent.

No open issues 🎉

What changed in this PR

This PR reorganizes the mxalign package so that the configuration-driven verification pipeline lives under a single pipeline/ submodule. It is the final step in a stacked refactor series (#39, #40) that reshapes the top level into accessor, alignment, and pipeline (plus the shared utils). The cli, runner, verification, and transformations modules—together with the pipeline-only helpers config, dates, and save—move into pipeline/, while utils/ retains only projections and traits used by accessor and alignment.

Changes:

• Move cli.py, runner.py, verification.py, transformations/, and utils/{config,dates,save}.py into pipeline/, updating relative imports (e.g. runner now imports ..alignment.time/..alignment.nans and .config/.save/.verification).
• Update the public surface: mxalign/__init__.py re-exports the same functions and lists accessor/alignment/pipeline in __all__; console script becomes mxalign.pipeline.cli:main.
• Update tests, README.md, and examples/advanced.ipynb to the new import paths.

File	Description
src/​mxalign/​__init__.py	Re-exports public API from new paths; __all__ → accessor/alignment/pipeline
src/​mxalign/​pipeline/​__init__.py	New package init importing transformations so they register on import
src/​mxalign/​pipeline/​cli.py	Moved CLI; lazily imports .runner
src/​mxalign/​pipeline/​runner.py	Moved runner; imports updated to .config/.save/.verification and ..alignment.*
src/​mxalign/​pipeline/​verification.py	Moved Metric/verify; imports .transformations.external
src/​mxalign/​pipeline/​config.py	Moved config loader; imports .dates
src/​mxalign/​pipeline/​dates.py	Moved date-range helper
src/​mxalign/​pipeline/​save.py	Moved dataset/metrics save helpers
src/​mxalign/​pipeline/​transformations/​*.py	Moved transformation registry/base/external/transform modules
src/​mxalign/​alignment/​*.py, alignment/​interpolations/​*.py	Alignment/interpolation modules (from stacked #39/#40) with corrected relative imports
src/​mxalign/​accessor/​*.py	Accessor package importing ..alignment ops (from stacked #40)
src/​mxalign/​accessors/​*.py, align/​space.py	Old modules removed as part of the move
pyproject.toml	Console script → mxalign.pipeline.cli:main
README.md, examples/​advanced.ipynb	Updated Runner import to mxalign.pipeline.runner
tests/​test_*.py	Updated imports and logger name to new module paths

_{Review effort: Balanced}

[mpvginde]

@leifdenby this also needs a rebase I guess