add xml to yaml converter for gemini gems

[mlee03]

Describe your changes

This PR creates an agent directory and a gem subdirectory containing the instructions used in
Gemini fre-xml-to-yaml-converter Gem

Issue ticket number and link (if applicable)

Fixes #XXX (replace XXX with the issue number and GitHub will autolink the PR to the issue)

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

Note: If you are a code maintainer updating the tag or releasing a new fre-cli version, please use the release_procedure.md template. To quickly use this template, open a new pull request, choose your branch, and add ?template=release_procedure.md to the end of the url.

[ilaflott]

this should be a pretty easy merge+review, can you add to the ok-unknown-words list?

[mlee03]

@singhd789, what do you think about this platforms section?

[singhd789]

I'll be reading this today, sorry this slipped under the radar

[thomas-robinson]

Your gem needs to add this to these fre properties to the model yaml:

  - &FMSIncludes "-IFMS/fms2_io/include -IFMS/include -IFMS/mpp/include"
  - &MOMIncludes "-Iocean/MOM6-examples/src/MOM6/pkg/CVMix-src/include -Iocean/MOM6-examples/src/MOM6/src -Iocean/MOM6-examples/src/MOM6/src/framework"

The MOMIncludes will be dependent on where MOM is cloned. In this case, I had this:

    <component name="mom6" requires="fms" paths="mom6/src/MOM6/config_src/{infra/FMS2,memory/dynamic_nonsymmetric,drivers/FMS_cap} mom6/src/MOM6/src/{*,*/*} mom6/src/MOM6/config_src/external/{ODA_hooks,database_comms,drifters,stochastic_physics,MARBL} ocean_BGC/generic_tracers ocean_BGC/mocsy/src ">
       <source versionControl="git" root="https://github.com/NOAA-GFDL">
        <codeBase version="main"> ocean_BGC.git </codeBase>
        <csh><![CDATA[
          ( cd ocean_BGC && git checkout $(OCEAN_BGC_GIT_TAG) )
	  git clone -b dev/gfdl https://github.com/NOAA-GFDL/MOM6-examples.git mom6
	  pushd mom6
	  git checkout $(MOM6_GIT_TAG)
	  git submodule update --recursive --init src/MOM6 src/SIS2 src/icebergs

          (cd src/icebergs && git checkout dev/gfdl)
          popd

          pushd mom6
          set platform_domain = `perl -T -e "use Net::Domain(hostdomain) ; print hostdomain"`
          if ("${platform_domain}" =~ *"MsState"* ) then
            ln -s /work/noaa/gfdlscr/pdata/gfdl/gfdl_O/datasets/ .datasets
          else
            ln -s /gpfs/f5/gfdl_o/world-shared/datasets .datasets
          endif
          popd

          test -e mom6/.datasets
          if ($status != 0) then
            echo ""; echo "" ; echo "   WARNING:  .datasets link in MOM6 examples directory is invalid"; echo ""; echo ""
          endif


        ]]></csh>
      </source>
      <compile>
        <cppDefs><![CDATA[ $(F2003_FLAGS) -DMAX_FIELDS_=100 -DNOT_SET_AFFINITY -D_USE_MOM6_DIAG -D_USE_GENERIC_TRACER -DUSE_PRECISION=2 ]]></cppDefs>
        <makeOverrides>OPENMP=""</makeOverrides> <!-- openmp switch for MOM6 may cause crash -->
      </compile>
    </component>

and consolidated the two ocean repos into a single ocean component like this:

    - component: "ocean"
      requires: ["FMS"]
      repo: ["https://github.com/NOAA-GFDL/ocean_BGC.git","https://github.com/NOAA-GFDL/MOM6-examples.git"]
      branch: [*OCEAN_BGC_GIT_TAG,"dev/gfdl"]
      paths:
        - "ocean/MOM6-examples/src/MOM6/config_src/infra/FMS2"
        - "ocean/MOM6-examples/src/MOM6/config_src/memory/dynamic_nonsymmetric"
        - "ocean/MOM6-examples/src/MOM6/config_src/drivers/FMS_cap"
        - "ocean/MOM6-examples/src/MOM6/src/*"
        - "ocean/MOM6-examples/src/MOM6/src/*/*"
        - "ocean/MOM6-examples/src/MOM6/config_src/external/ODA_hooks"
        - "ocean/MOM6-examples/src/MOM6/config_src/external/database_comms"
        - "ocean/MOM6-examples/src/MOM6/config_src/external/drifters"
        - "ocean/MOM6-examples/src/MOM6/config_src/external/stochastic_physics"
        - "ocean/MOM6-examples/src/MOM6/config_src/external/MARBL"
        - "ocean/ocean_BGC/generic_tracers"
        - "ocean/ocean_BGC/mocsy/src"
      additionalInstructions: !join [
        "\n",
        " cd ocean/MOM6-examples \n",
        " git checkout ",*MOM6_GIT_TAG,"\n",
        " git submodule update --recursive --init src/MOM6 src/SIS2 src/icebergs \n",
        " cd src/icebergs \n",
        " git checkout dev/gfdl \n",
        " cd ../../../ \n",
        "            ln -s /gpfs/f5/gfdl_o/world-shared/datasets .datasets\n",
        "            echo \"\"; echo \"\" ; echo \"    WARNING:  .datasets link in MOM6 examples directory is invalid\"; echo \"\"; echo \"\"\n"
      ]
      cppdefs: !join [*F2003_FLAGS, " -DMAX_FIELDS_=100 -DNOT_SET_AFFINITY -D_USE_MOM6_DIAG -D_USE_GENERIC_TRACER -DUSE_PRECISION=2 "]
      makeOverrides: 'OPENMP=""'
      otherFlags: !join [*FMSIncludes," ", *MOMIncludes]

and needs to add this to each component:

      otherFlags: !join [*FMSIncludes," ", *MOMIncludes]

[ceblanton]

Looks great!

Will this convert postprocessing XMLs to Yamls?

How can users use that Gem markdown file? (I'll serve as your naive user)

[mlee03]

@thomas-robinson 😱

[mlee03]

@thomas-robinson, blurb about FMSIncludes MOMIncludes

[mlee03]

@thomas-robinson , otherFlags instructions. This can be changed to add FMSIncludes and MOMIncludes regardless of dependencies