atmos_phys

This is the repository that combines the atmosphere physics and chemistry

Table of contents

• Guidelines for Contributing
• Instructions on merging in code from atmos_param or atmos_shared
• XML changes to checkout atmos_phys

Guidelines for Contributing

If you have code you would like to contribute, you will first create a git branch. Your branch should be in the format of /user/ini/BranchName where ini are your initals and BranchName is a name that describes the purpose of your branch. Avoid using a BranchName like bugfix or update because this is not descritive.

git checkout -b user/ini/BranchName

Second, you will commit your changes, and push them to the atmos_phys remote repository.

git push -u origin user/ini/BranchName

After the changes are pushed, you can share your code with others. If your code should be included in the main model development, you can submit a merge request by clicking on the Merge Requests link on the gitlab page. Please include a detailed description of the changes made by your branch. You should submit the merge to the main development branch (master). Assign your merge request to Uriel Ramirez.

Instructions on merging in code from atmos_param or atmos_shared

In order to commit changes that currently exist on atmos_param or atmos_shared, you first have to commit and push the changes to a branch in the repository you are working in. Next you will clone atmos_phys. After that, you will add the original repository to as a remote in your atmos_phys directory. You can then fetch from the original repository and merge in the branch you were working on.

Below is an example set of instructions to accomplish this. This assumes that you cloned atmos_param.

git clone https://gitlab.gfdl.noaa.gov/fms/atmos_phys.git #clone atmos_param
cd atmos_phys 
pushd ../atmos_param/ #Set up a directory stack with the two repo directories
git checkout user/ter/exampleBranch #check out your user branch
git fetch #fetch any changes that may have occurred in atmos_param since you branched
git pull origin/master #merge in the master (update your code base)
## The following 3 lines can be skipped if you already have committed changes ##
touch test.file #Make your changes (DO NOT COPY THIS, it is just an example)
git add test.file #stage your changes
git commit -m "Save a test commit to user branch" #commit your changes
## The folowing can be skipped if you have already pushed your changes ##
git push -u origin user/ter/exampleBranch
pushd #change directory to the atmos_phys folder
git checkout -b user/ter/exampleBranch #create your branch in atmos_phys
git remote add param https://gitlab.gfdl.noaa.gov/fms/atmos_param.git #add atmos_param as a remote
git fetch param #fetch the contents of the atmos_param
git merge param/user/ter/exampleBranch #merge your branch from atmos_param into your branch on atmos_phys
git push -u origin user/ter/exampleBranch

A note on git remotes:

The default name for a remote is origin. When you clone a repository, the remote is automatically given the name origin. When you add a remote, you can name it anything except origin. In the above example, I named the remote param. That's why I fetch from param. To see what remotes you have set up, you can issue the command

git remote -v

XML changes to checkout atmos_phys

There are a few modifications to an XML in order switch to the atmos_phys code. An XML will have a section in the compile experiment that looks like the following:

    <component name="atmos_phys" requires="fms" paths="atmos_param atmos_shared">
      <description domainName="" communityName="" communityVersion="$(RELEASE)" communityGrid=""/>
      <source versionControl="git" root="http://gitlab.gfdl.noaa.gov/fms">
        <codeBase version="$(RELEASE)"> atmos_shared.git atmos_param.git </codeBase>
          <csh><![CDATA[
            ( cd atmos_shared && git checkout $(ATMOS_GIT_TAG) )
            ( cd atmos_param  && git checkout $(ATMOS_GIT_TAG) )
           ]]>
          </csh>
      </source>
      <compile>
        <cppDefs>$(F2003_FLAGS) -DCLUBB</cppDefs>
      </compile>
    </component>

This can be found by searching the XML for atmos_phys or atmos_shared.git or atmos_param.git. This block should be updated to the following:

    <component name="atmos_phys" requires="fms" paths="atmos_phys">
      <description domainName="" communityName="" communityVersion="$(RELEASE)" communityGrid=""/>
      <source versionControl="git" root="http://gitlab.gfdl.noaa.gov/fms">
        <codeBase version="$(RELEASE)"> atmos_phys.git </codeBase>
          <csh><![CDATA[
            ( cd atmos_phys  && git checkout $(ATMOS_GIT_TAG) )
           ]]>
          </csh>
      </source>
      <compile>
        <cppDefs>$(F2003_FLAGS) -DCLUBB</cppDefs>
      </compile>
    </component>

1. The paths has been changed from "atmos_param atmos_shared" to "atmos_phys".
2. The codeBase was changed from atmos_shared.git atmos_param.git to atmos_phys.git
3. The csh block was updated to only cd to atmos_phys

NOTE: Users should switch to atmos_phys if they are checking out code that is newer than xanadu. If your model is running code older than xanadu, you should check the code out from atmos_shared and atmos_param.