Script to run cycling DA using JEDI in cube sphere space, and offline Noah-MP model in vector space.

Clara Draper, Nov, 2021.

To install and build:

1. Fetch sub-modules.

git submodule update --init

2. Compile sub-modules.

cd vector2tile then follow instructions in README. cd ..

cd ufs-land-driver git submodule update --init configure select 2 make

cd landDA_workflow then follow instructions in README.

3. Put vector restart in this directory.

filename example:ufs_land_restart.2015-09-02_18-00-00.nc

4. Set start and end dates in analdates.sh

5. Set directories and DA options at top of submit_cycle.sh

To run:

submit_cycle.sh

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• Submitting pull requests to offline_land_workflow

1. Each pull request should have an associated issue. Create a draft pull request as soon as you start working on a new issue, and select the "DRAFT: do not merge" option from the labels. You should then regularly push commits to your branch, making sure to provide a useful description of the commit in the comments.

2. Before doing the final push, make sure that any directories / variable values that you changed to run the code are changed back to their orginal values. Each script has a line that says something like "you shouldn't have to change anything below here" - this marks the end of the user-specified varuiables. In your PRs the user-specified variable should not be changed (so don't change the values of variables above that line).

3. Before doing the final push, edit your .gitmodules to point at the original repos, and not to your version.

4. Make sure that your added code does not affect the pre-existing code capabailities (regression test will be added soon).

5. Try to minimize unnecessary moving code around / reformatting code / changing script names.

6. Give your PR a name that clearly identifies it. Likewise, give your branches identifying names.

7. Add comments to the PR briefly listing all the changes that have been made (i.e. 'fixed bug in WHATEVER_VARIABLE, added SMAP observation assimilation, ...').

8. If you need to submit PRs to multiple repos, give them the same name and note in the comments that they're linked.

9. As you prepare the PR, you will have an option to see your changes. Use this to double-check everything (and to make sure you've done 1 and 2 above).

• To clone and commit code with submodules

1. using the web interface, fork any modules that you will be editing.

2. create a branch within your fork, with an informative name ( use this format: feauture/BRANCH_NAME, or bugfix/BRANCH_NAME)

3. clone the parent repo and update the .gitmodules to point to your code

git clone YOUR_REPO cd YOUR_REPO update .gitmodules to point to your forks/branches git submodule update --init --recursive

(note: landDA_workflow also has submodules. same process for .gitmodules in that repo if you need to change these).

4. Make your code changes.

5. commit changes to each submodule, starting at the lowest level and working your way up (to the parent repo).

If you have committed changes to a submodule, you will need to commit the updated submodule in the parent module.

cd SUBMODULE git add FILES git commit cd .. git add SUBMODULE <-- here. git commit

6. when pushing your updates, this option is useful to check that the necesary submodules have been pushed:

git push --recurse-submodules=check

• To merge the latest remote changes into your local clone:

Note that the submodules are cloned as a specific hash of their branch. This has is not necessarily the head of the branch. When merging the latest remote upcates you need to merge to the submodules hash used by the parent repo, not to the head of the submodule branch (see below). Also, if you want to edit the submodules, switch to a branch immediately (otherwise, it's a nuisance to do this later).

This is clunky, but the best way I've found to do it is to clone the module that you wish to update to, then go to each submodule and check the hash. "git log" will show you the commit history, including the hash (the long string of letters and numbers) of the latest commit. For each submodule that you've edited, manually merge the latest hash into your local version:

check have remote set, and if not add

git remote -v git remote add upstream MAIN_REPO git fetch upstream git checkout YOUR_LOCAL_BRANCH git merge REMOTE_REPO_HASH

For submodules that you haven't edited, you can just checkout the HASH ("git fetch" first to download it).