Add cli to downscaling (#18)

* first pass pre-test

* Add magic-downscaling CLI: prepare/cluster/extract/downscale/analyze
verbs - tested on pecan env ver 1.10

* re-org of verbs, split of demo data obtain, and correction so that
prepare can be run ahead of other verbs.

* update to run_script and check_r_libraries to correctly determine exit
status to identify step failure/success.

* fixes to sourcing of helper functions, previously covered by sourcing
config, now covered by sourcing specific files.

* - actually added intended code to wire CLI together
- correctly reads steps from workflow manifest via get_steps_array
- handles input scalar parameters and path parameters via resolve_param
  and resolve_path respectively
  -- inputs and outputs are paths
  -- params are scalars
- dynamically builds command arguments from specified inputs,outputs,
  and params
- command-line parameter names are the keys (e.g., raw_data_dir -->
  '--raw_data_dir')
- the values in the manifest are passed as values to the specified key
  (raw_data_dir: 'data_raw')
- demo workflow completes as normal
- CI basics for demo workflow in place: needs repo config to actually
  work.

* Fix PR review issues: config keys, r_libraries, CI, manifest validation

- Move aws_profile from downscaling: to global: in
  example_user_config.yaml
  and .github/ci/downscaling_ci_config.yaml; fix magic-downscaling's
  stale
  help text to match the code, which already read global.aws_profile
- Correct r_libraries across all 11 manifest steps (cluster/extract/
  downscale/analyze) against actual script imports, including sourced R/
  helpers: add missing hard deps (here, knitr, magick, units, withr,
  ClusterR, PEcAn.utils, future, lubridate, arrow, janitor, jsonlite,
  randomForest, iml, vroom, patchwork, scales, PEcAn.data.land), drop
  confirmed-unused ones (caladaptr from prepare_anchor_sites; sf, furrr
  from cluster_sites; sf from subsample_design_points)
- Drop unused AWS_ACCESS_KEY_ID/AWS_SECRET_ACCESS_KEY/AWS_DEFAULT_REGION
  env exports from the CI workflow; --profile magic already resolves
  credentials on the runner, so those secrets were dead weight
- Fix check_r_libraries capturing stderr into the same variable as the
  package-availability check's stdout, which could misreport stray
  stderr
  (e.g. locale warnings) as a missing package; capture stderr separately
  so it's only surfaced on a genuine Rscript failure
- Delete unused .Renviron.bak / .Rprofile.bak (nothing in the repo reads
  either file; leftover from the pre-conda renv setup)
- Remove the dangling docs/manifest-driven-cli-design.md reference from
  downscaling_manifest.yaml (that doc is intentionally not tracked)
- Drop the "placeholder name" parenthetical from the cluster verb's help
  text now that the name is settled
- Make get_steps_array validate that every manifest step has both
  `script`
  and `name`, failing fast with the offending step's index/script
  instead
  of silently misaligning STEPS/STEP_NAMES (dispatch elsewhere is
  name-keyed via `select(.name == ...)`, so a missing name breaks that
  lookup silently otherwise)
- Sweep scripts/*.R: replace the copy-pasted stop() calls for --run_dir/
  --mode validation with PEcAn.logger::logger.severe(), matching house
  logging style
- Fix get-demo-data help text to say demo-data/ lands relative to the
  invocation directory, not "the repo root" (matching actual
  INVOCATION_CWD-based behavior)

* Resolve PR #18 review feedback: disconnect cluster verb, trim manifest
cruft

- Fixed: cluster verb removed from CLI, scripts left as non-CLI tools
- Fixed: 031 (mixed-system aggregation) excluded from extract step
- Fixed: dead placeholder path keys removed (prepare_dir, extract_dir,
  downscaled_csv, county_totals_csv, analyze_dir, aggregated_output_csv)
- included data resources for github ci

* add readme update

* wired in the n_cores parameter is 030 and 040. used config to set
n_cores, but falls back to environment variables from slurm as needed.

* Apply suggestion from @dlebauer

---------

Co-authored-by: David LeBauer <dlebauer@gmail.com>

Author: hdpriest-ui

.Renviron

@@ -0,0 +1,12 @@
+# CI config for test-downscaling-demo.yml — same shape as example_user_config.yaml,
+# with an isolated run_dir so CI runs don't collide with local dev-run dirs.
+
+global:
+  run_dir: "ci-downscaling-rundir/"
+  aws_profile: magic
+
+downscaling:
+  mode: demo
+  pecan_output_dir: "demo-data/modelout/ccmmf_phase_3_scenarios_v2_n2o_ch4"
+  data_layers_dir: "demo-data/data"
+  anchor_site_locations: "data_raw/anchor_site_locations.csv"

.Rprofile

@@ -0,0 +1,28 @@
+site_id,lat,lon,external_site_id,site_name,crops,pft
+26336,36.17114,-120.19718,US-ASH,San Joaquin Valley Almond High Salinity,Almond,woody perennial crop
+159849,36.94729,-120.10535,US-ASL,San Joaquin Valley Almond Low Salinity,Almond,woody perennial crop
+534243,36.1778,-120.20411,US-ASM,San Joaquin Valley Almond Medium Salinity,Almond,woody perennial crop
+169473,36.23738,-119.92755,US-PSH,San Joaquin Valley Pistachio High Salinity,Pistachio,woody perennial crop
+557284,36.82778,-120.13963,US-PSL,San Joaquin Valley Pistachio Low Salinity,Pistachio,woody perennial crop
+328163,38.09936,-121.50154,US-Bi1,Bouldin Island Alfalfa,Alfalfa,herbaceous crop
+565118,38.10958,-121.53613,US-Bi2,Bouldin Island Corn/Sorghum,"Corn, Sorghum",herbaceous crop
+522375,32.81281,-115.44207,US-Dea,UC Desert REC Alfalfa,Alfalfa,herbaceous crop
+205678,38.13153,-121.55174,US-DS1,Staten Corn 1,Corn,herbaceous crop
+592578,38.13799,-121.51401,US-DS2,Staten Corn 2,Corn,herbaceous crop
+413887,38.12346,-121.54982,US-DS3,Staten Rice 1,Rice,herbaceous crop
+590334,36.35733,-119.09283,US-Lin,Lindcove Orchard,Oranges,woody perennial crop
+440393,39.57712,-121.86221,US-RGB,Butte County Rice Farm,Rice,herbaceous crop
+420343,37.69949,-121.1391,US-RGF,Stanislaus Forage Farm,Forage crops,herbaceous crop
+132390,39.59614,-122.0226,US-RGG,Glenn County Rice Farm,Rice,herbaceous crop
+218534,38.1741,-121.50302,US-Si1,Staten Island Fallow,Fallow,non crop
+52519,38.17441,-121.51733,US-Si2,Staten Island Flooded,Rice,herbaceous crop
+248496,38.11573,-121.64507,US-Tw3,Twitchell Alfalfa,Alfalfa,herbaceous crop
+296871,38.54294,-121.87237,russell-ranch,Russell Ranch,"tomato, corn, wheat",herbaceous crop
+16073,38.50244,-121.97646,wolfskill,Wolfskill Experimental Orchards,Fruit and nut breeding,woody perennial crop
+415399,33.96684,-117.34049,ucr-citrus,UC Riverside Citrus Research,Citrus variety collection,woody perennial crop
+589918,36.62289,-121.54925,salinas_socs,USDA-ARS Salinas Organic Cropping Systems,"Romaine lettuce, broccoli",herbaceous crop
+514070,37.62903,-121.08781,modesto_almond_usda,USDA-ARS Modesto almond fertigation trial,Almond,woody perennial crop
+535358,39.68222,-122.0026,US-RGO,Glenn County Organic Rice,Organic rice,herbaceous crop
+589581,38.09222,-121.64036,US-Tw2,Twitchell Corn,Corn,herbaceous crop
+590073,38.10809,-121.65527,US-Twt,Twitchell Island Rice,Rice,herbaceous crop
+452888,36.34204,-120.1055,west-side,West Side Research Center,Row crops including cotton,herbaceous crop