Single python script2

[nhsavage]

change the top level driver script to be python based

[Eleanor-Dean]

This is still not working right for me -->
unless im missing the intention, the ./{base} in the config yml + the mkdir in the run_all.py are making the scratch directory in the OSOP file system.

If this is intentional thats fine but I fear it is because the pythonpath is now linked to the osop root - it makes it so when you run any code it attempts to commit the changes. Straight run with no flags caused vs code git hub to suggest commiting 627 files.

TLDR:
the outputs appear under --> osop/scripts/outputs. Causing file backlog when running

[Copilot]

Pull request overview

This PR replaces the legacy top-level shell orchestration with a Python-based runner (scripts/run_all.py) driven by a single YAML configuration file (osop_config.yml), and updates documentation/tests accordingly.

Changes:

• Add a Python orchestrator (scripts/run_all.py) that executes existing workflow steps via subprocesses using a YAML config.
• Add comprehensive pytest coverage for config parsing/validation and pipeline command construction (scripts/tests/test_run_all.py).
• Remove legacy shell runners and an unused downloader script; update user documentation (docs/source/run.md).

Reviewed changes

Copilot reviewed 9 out of 9 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
scripts/tests/test_run_all.py	New unit tests for the Python orchestrator (config validation + pipeline behavior via mocking).
scripts/run_all.sh	Removes the legacy bash top-level runner.
scripts/run_all.py	Adds the new Python top-level orchestrator replacing the shell runner.
scripts/output/single_script/logfiles/download_log_total_precipitation_meteo_france_5_2026-07-31_09:41:26.txt	Adds a captured runtime log output (likely unintended repo artifact).
scripts/get_any_hc_fc_iri.py	Removes a deprecated/unused downloader script.
scripts/all_mons_precip_array.sh	Removes legacy SLURM/bash array runner.
scripts/all_mons_array.sh	Removes legacy SLURM/bash array runner.
osop_config.yml	Adds the default YAML configuration file consumed by the new runner.
docs/source/run.md	Updates “Running the toolkit” docs to the new Python + YAML entrypoint.

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[github-actions]

Coverage Report

File	Stmts	Miss	Cover	Missing
lib/osop
compare_terciles.py	76	76	0%	9–336
compute_products_func.py	134	134	0%	8–449
compute_scores_func.py	154	154	0%	17–414
ens_plotting.py	142	54	62%	112–148, 240, 250, 318–337, 357–418
plot_verify.py	173	145	16%	89–126, 158–249, 276–309, 339–434, 458–535
pycpt_convert.py	394	287	27%	76–99, 116–122, 140, 163–169, 189–205, 219–225, 242–270, 290, 311–313, 340–531, 554, 569–571, 663, 736–744, 759–765, 776–791, 796–799, 804–808, 816–827, 843–897, 917–971, 1009–1044
run_pycpt.py	126	126	0%	11–362
util.py	59	12	80%	89, 103, 131, 159–172, 179–184
TOTAL	1574	988	37%

Tests	Skipped	Failures	Errors	Time
101	0 💤	0 ❌	0 🔥	13.239s ⏱️

[Eleanor-Dean]

Approved with notes discussed:
--> need to resolve services/centres list so test runs can be easy
--> need to remove some of the terminal output (to verbose)
--> need to set up some regard to coping with the warnings so we dont just forget about them
--> need to do the windows test run
--> need to edit documentations
--> Open above as issues

[nhsavage]

Approved with notes discussed: --> need to resolve services/centres list so test runs can be easy --> need to remove some of the terminal output (to verbose) --> need to set up some regard to coping with the warnings so we dont just forget about them --> need to do the windows test run --> need to edit documentations --> Open above as issues

simple ones covered by #188 , services/centres list clean up already has #183

only missing issue now

• need to set up some regard to coping with the warnings so we dont just forget about them