split prep_ngen_data into steps

[JordanLaserGit]

WIP — opening this to get feedback on a refactor idea before taking it further.

prep_ngen_data in processor.py had grown to ~700 lines and was hard to follow. This is particularly a problem for anyone looking to work on/contribute to this code base.

This PR splits prep_ngen_data into an init step followed by named sequential steps, so the top-level function has much of the details abstracted out. This PR should not change functionality and is a pure refactor (besides maybe addressing a few bugs along the way).

Additions

• config.py
• writers.py
• metadata.py
• utils.py
• Geometry / Extracted / WriteResult dataclasses to carry state between steps

Removals

• All 16 module-level globals prep_ngen_data used to set
• Duplicated forcings / channel_routing metadata dicts (identical keys, differed only in nvars_intput / nvars_output)

Changes

• prep_ngen_data is now: read_config → build_output_layout → parse_nwm_filenames → load_geometry → write_run_manifest → extract → write_outputs → plot → collect_metadata → tar
• data_source branching pushed down into named per-mode functions instead of ~20 inline if data_source == checks
• processor.py: 1686 → 748 lines

Testing

All pytests pass besides unmerged fix for test_restart, pre-existing upstream off-by-one, unrelated to this PR)

Screenshots

Notes

• Anything that hardcoded the old double-slash S3 metadata path will need updating.

Todos

• Possible follow-up: split into three top-level entry points per data_source, since the troute_restarts path shares almost nothing with forcings

Checklist

• PR has an informative and human-readable title
• Changes are limited to a single goal
• Code can be automatically merged
• Code follows project standards
• Passes all existing automated tests
• Any change in functionality is tested
• New functions are documented
• Placeholder code is flagged / future todos are captured in comments
• Visually tested in supported browsers and devices
• Project documentation has been updated
• Reviewers requested with the Reviewers tool ➡️

Testing checklist

Target Environment support

• Windows
• Linux
• Browser

Accessibility

• Keyboard friendly
• Screen reader friendly

Other

• Is useable without CSS
• Is useable without JS
• Flexible from small to large screens
• No linting errors or warnings
• JavaScript tests are passing

[quinnylee]

This is awesome and much more readable! Glad the global variables are gone. I really like the usage of the dataclasses to store our variables, maybe the config one can be used as an argument in the writers.py module to reduce the number of arguments passed around?

I tried to have three separate entry points for eachdata_source while I was hand-refactoring, but I found that there were just enough differences in the ways each function was called for each case that I wasn't able to neatly reuse functions. Or maybe I just didn't put enough time into it. Anyway, I don't think the three entry points are necessary for readability

[JordanLaserGit]

I'm happy with any idea that reduces inputs args!

An idea I have for this in relation to the community contribution docs I'm working on, is it would be nifty to be able to link conceptually relevant portions of the code base in those docs.

For instance, the core processing function for forcings is forcing_grid2catchment() and this could be split into a few descriptively named functions with verbose comments describing the code. This effort would be entirely for visibility for contributors so they could readily look into the code and see what is scientifically relevant in this heap of a repository. Might be tricky just linking the line numbers, so maybe worth splitting into it's own file so we can reference reliably?

[quinnylee]

We could also auto-generate API docs with links to source code if that would help with community contribution. Something like https://numpy.org/doc/stable/reference/generated/numpy.isdtype.html

So if we do break up big functions into little functions with good docstrings, those could accomplish the goal of exposing relevant sections through autogenerated API docs.

This could also be a chance for us to "privatize" our internal functions that may never change/get reused.

[JordanLaserGit]

@quinnylee I think that's a great idea. I can focus on breaking up forcing_grid2catchment() and others into scientifically relevant functions and probably stick them all in one file to be imported by the modules that need them.

I have the initial community contribution docs PR up here. I'm thinking the section "Alternative catchment averaging and weight generation" in CONTRIBUTING.md would contain the links we are talking about here.

[Copilot]

Pull request overview

Refactors the main prep_ngen_data pipeline by splitting configuration, geometry loading, extraction, writing, plotting, metadata collection, and tar packaging into named steps and new helper modules, aiming to preserve existing behavior while making the flow easier to follow and maintain.

Changes:

• Introduces config.py, writers.py, and metadata.py to encapsulate config parsing/output layout, output writing, and run-statistics generation.
• Reworks processor.py into a step-based orchestration using new Geometry / Extracted / WriteResult dataclasses.
• Stabilizes tests by restoring shared module-level configuration state between test cases via an autouse fixture.

Reviewed changes

Copilot reviewed 14 out of 14 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
tests/test_forcingprocessor.py	Adds autouse fixture to reset mutated shared conf between tests.
tests/test_channelrouting.py	Adds autouse fixture to reset mutated shared conf between tests.
src/forcingprocessor/writers.py	New module for dataframe/netcdf/tar writing and multiprocessing orchestration.
src/forcingprocessor/weights_hf2ds.py	Import cleanup, typing tweaks, and small runtime hardening (timeouts, cpu_count guard).
src/forcingprocessor/utils.py	Adds shared helpers (phase timing, JSON/dataset readers, work distribution/load balancing).
src/forcingprocessor/troute_restart_tools.py	Adds typing ignore for boto3 client creation.
src/forcingprocessor/subset_conus_vpus.py	Import cleanup and minor refactors/formatting.
src/forcingprocessor/processor.py	Major refactor: step-based pipeline + new dataclasses + delegates to config/writers/metadata.
src/forcingprocessor/plot_forcings.py	Typing improvements, safer defaults, and minor refactors to plotting helpers/CLI.
src/forcingprocessor/nwm_filenames_generator.py	Improves file loading hygiene (encoding, variable naming).
src/forcingprocessor/metadata.py	New module for metadata/statistics frame generation and output writing.
src/forcingprocessor/medium_range_time_ax_mod.py	Docstring/header cleanup, constant naming, and typing adjustments.
src/forcingprocessor/config.py	New module for config parsing/validation, output layout, and run manifest writing.
src/forcingprocessor/channel_routing_tools.py	Minor cleanup and typing ignore for boto3 client creation.

Suppressed comments (1)

src/forcingprocessor/processor.py:613

• Spelling: the status message says "processs" (extra 's'), which looks unintentional and makes logs harder to scan.

        print(
            f"\n\nWrite processs: {cfg.nprocs}\nWrite time: {write_time:.2f}" +
            f"\nWrite rate {geom.ncatchments / write_time:.2f} files/second\n",

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[quinnylee]

Sorry this has ballooned into an absolute monster of a branch. Let me know what you all think of the changes. Will be more than happy to revert (or you can go ahead and do it yourself since i'll be at conferences for like two weeks straight) if you think any of them are not useful!!