697.workflow checkout tool by singhd789 · Pull Request #736 · NOAA-GFDL/fre-cli

singhd789 · 2026-02-11T15:18:33Z

Describe your changes

transfer fre pp checkout functionality to fre workflow checkout
add "workflow" section to the settings yaml (for now) to define a repo and branch to use for the pp workflow (and eventually the run workflow)
add fre/workflow folder with freworkflow.py, tests/, checkout_script.py, README.md
add "workflow" tool to fre.py

Issue ticket number and link (if applicable)

#697

Checklist before requesting a review

I ran my code
I tried to make my code readable
I tried to comment my code
I wrote a new test, if applicable
I wrote new instructions/documentation, if applicable
I ran pytest and inspected it's output
I ran pylint and attempted to implement some of it's feedback
No print statements; all user-facing info uses logging module

…rkflow-checkout-tool

…DL/fre-cli into 697.workflow-checkout-tool

codecov · 2026-02-12T21:37:09Z

Codecov Report

❌ Patch coverage is 90.90909% with 12 lines in your changes missing coverage. Please review.
✅ Project coverage is 84.36%. Comparing base (ad432b1) to head (6ce4930).

Files with missing lines	Patch %	Lines
fre/workflow/checkout_script.py	83.56%	12 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #736      +/-   ##
==========================================
+ Coverage   84.08%   84.36%   +0.28%     
==========================================
  Files          70       73       +3     
  Lines        4775     4906     +131     
==========================================
+ Hits         4015     4139     +124     
- Misses        760      767       +7

Flag	Coverage Δ
unittests	`84.36% <90.90%> (+0.28%)`	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
fre/__init__.py	`100.00% <100.00%> (ø)`
fre/fre.py	`100.00% <ø> (ø)`
fre/workflow/freworkflow.py	`100.00% <100.00%> (ø)`
fre/workflow/tests/test_checkout_script.py	`100.00% <100.00%> (ø)`
fre/workflow/checkout_script.py	`83.56% <83.56%> (ø)`

... and 2 files with indirect coverage changes

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- Use TMPDIR env variable if command line option not passed

…rkflow-checkout-tool

singhd789 · 2026-02-25T21:15:47Z

Note: related PR --> NOAA-GFDL/gfdl_msd_schemas#45 (we'll get the schema PR in first so I can bring in the changes to the submodule here)

ilaflott

is this replacing any functionality elsewhere- i.e. fre pp checkout? if so, the deprecated code should be id'd for removal

singhd789 · 2026-02-26T15:33:03Z

is this replacing any functionality elsewhere- i.e. fre pp checkout? if so, the deprecated code should be id'd for removal

YES! Thank you for that reminder

fre/workflow/checkout_script.py

ilaflott · 2026-02-26T15:45:15Z

fre/workflow/checkout_script.py

+    if not Path(f"{src_dir}/{workflow_name}").is_dir():
+        fre_logger.info("Workflow does not yet exist; will create now")
+        create_checkout(repo = repo,
+                        tag = tag,
+                        src_dir = src_dir,
+                        workflow_name = workflow_name)
+    elif Path(f"{src_dir}/{workflow_name}").is_dir() and force_checkout:
+        fre_logger.warning(" *** PREVIOUS CHECKOUT FOUND: %s/%s *** ", src_dir, workflow_name)
+        # Remove checked out repo
+        shutil.rmtree(f"{src_dir}/{workflow_name}")
+        fre_logger.warning(" *** REMOVING %s/%s *** ", src_dir, workflow_name)
+        # Redo checkout
+        create_checkout(repo = repo,
+                        tag = tag,
+                        src_dir = src_dir,
+                        workflow_name = workflow_name)


similar to my other comment, these three conditionals can likely be collapsed.

i think you're trying to be explicit with if/elif/else blocks, but when the blocks are too similar in functionality, that tends to create confusion as big similar blocks of code are actually hard to read for only the differences.

one thing you can do to simplify this block of flow control, is to put some of the features you want here on their own terms. example: if force_checkout is True, then you can check for the existence of f"{src_dir}/{workflow_name}" in it's own statement before this whole block, and remove it if so.

Ah yeah, ok so would it be better (or kind of the same) to have something like:

if Path(...).exists(): if force_checkout: (warnings and removing) else: (whole tag check logic) else: (actual checkout)

Oh that would definitiely get rid of the need for the def create_checkout function I added though 🎉

singhd789 · 2026-02-26T19:00:31Z

Note: I can also update the validate_yamls function that already lives in fre/yamltools/helpers and import/use that one here. However, that would require updating other files (like in fre make). They would probably be little changes BUT should I do that in another PR (to not add too much more here)? Or should I just get it over with in this PR?

singhd789 · 2026-02-26T19:34:35Z

is this replacing any functionality elsewhere- i.e. fre pp checkout? if so, the deprecated code should be id'd for removal

Opened an issue for removal: #760

Dana Singh and others added 12 commits January 27, 2026 15:42

#697 Add fre workflow checkout tool and test

0dc8622

#697 Comment out non-existent tools for now

099342f

#697 Comment out things that aren't done yet

40d43a5

#697 Add validation and update output file name for resolved yaml

440a040

#697 Add assert to test

3249384

Add comma

7c96c60

#697 Merge branch 'main' of github.com:NOAA-GFDL/fre-cli into 697.wo…

125b5e8

…rkflow-checkout-tool

#697 Add comma

b217d5e

#697 Merge branch '697.workflow-checkout-tool' of github.com:NOAA-GF…

0694409

…DL/fre-cli into 697.workflow-checkout-tool

#697 Put file moving in checkout creation

13ca73c

#697 See if pipeline run as root

70171a6

#697 Fix stat

c558027

Dana Singh added 2 commits February 12, 2026 17:52

#697 make it fail for a sec

60e73cc

test failure

38accb6

singhd789 linked an issue Feb 18, 2026 that may be closed by this pull request

FRE workflow checkout subtool #697

Open

Dana Singh and others added 14 commits February 18, 2026 09:35

#697 Add some readme content

06750f2

#697 Update comment

ecb3ed3

#697 Remove click branch overwrite

32d5906

#697 Comment out use of branch override

881366e

#697 Fix file permission test

8bef3ee

#697 Fix test

7d1eb4e

#697 hopfeully change file permissions correctly this time

516cf5d

#697 Nix file permission changes - doesn't work when running as root

95e25d8

#697 Address pylint messages

e3c2452

#697 Add fre workflow cli tests

7b1f816

#697 Some clean up

c48728b

#697 Add --force-checkout and --target-dir

817bf7a

#697 Update spacing to account for warning output

09afc2d

#697 Update documentation

a29645a

Dana Singh and others added 15 commits February 20, 2026 15:32

#697 Update doc

560093c

#697 Fix tests

10ce009

#697 Fix --target-dir click value

61be15c

- Use TMPDIR env variable if command line option not passed

#697 Add default dir (see if pipeline passes)

04e8985

#697 update

9daa391

#697 update

14e87e9

#697 Fix tests and update argument order

7af0425

#697 Merge branch 'main' of github.com:NOAA-GFDL/fre-cli into 697.wo…

c235bb4

…rkflow-checkout-tool

#697 fix exit code

5ee7f19

#697 Adjust spacing

007696d

#697 right spacing?

9ab07ca

#697 set TMPDIR

2d26bce

#697 Change warning to info

1af0992

#697 Update help message and other output

14c0d20

#697 Uncomment validation

ef0377b

singhd789 marked this pull request as ready for review February 25, 2026 22:55

singhd789 requested review from ceblanton, ilaflott and kiihne-noaa February 26, 2026 15:16

ilaflott reviewed Feb 26, 2026

View reviewed changes

ilaflott requested changes Feb 26, 2026

View reviewed changes

#697 Address ians comments

779b6ba

singhd789 requested a review from ilaflott February 26, 2026 19:34

#697 Update

6ce4930

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697.workflow checkout tool#736

697.workflow checkout tool#736
singhd789 wants to merge 45 commits intomainfrom
697.workflow-checkout-tool

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