#221 Merge branch 'main' of github.com:NOAA-GFDL/fre-cli into 221.fo…

…rce-checkout-and-compile

.github/workflows/build_conda.yml

@@ -11,6 +11,8 @@ jobs:
     steps:
       - name: Checkout Files
         uses: actions/checkout@v4
+        with:
+          submodules: 'recursive'
       - name: Run Conda to Build
         run: |
           conda config --append channels conda-forge

.github/workflows/create_test_conda_env.yml

@@ -7,16 +7,16 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
+        with:
+          submodules: 'recursive'
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
           python-version: '>=3.9'
-
       - name: Add conda to system path
         run: |
           # $CONDA is an env var pointing to root of miniconda dir
           echo $CONDA/bin >> $GITHUB_PATH
-      
       - name: Create fre-cli environment
         run: |
           # create environment containing all dependencies

.github/workflows/publish_conda.yml

@@ -11,6 +11,8 @@ jobs:
     steps:
       - name: Checkout Files
         uses: actions/checkout@v4
+        with:
+          submodules: 'recursive'
       - name: Run Conda to Build and Publish
         run: |
           conda config --append channels conda-forge

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "fre/gfdl_msd_schemas"]
+	path = fre/gfdl_msd_schemas
+	url = https://github.com/NOAA-GFDL/gfdl_msd_schemas

CONTRIBUTING.md

@@ -1,7 +1,7 @@
 ## **For Developers**
 
 * Developers are free to use this repository's `README.md` to familiarize with the CLI and save time from having to install any dependencies, but development within a Conda environment is heavily recommended regardless
-* Gain access to the repository with `git clone [email protected]:NOAA-GFDL/fre-cli.git` or your fork's link (recommended) and an SSH RSA key
+* Gain access to the repository with `git clone --recursive [email protected]:NOAA-GFDL/fre-cli.git` or your fork's link (recommended) and an SSH RSA key
     - Once inside the repository, developers can test local changes by running a `pip install .` inside of the root directory to install the fre-cli package locally with the newest local changes on top of the installed Conda fre-cli dependencies
     - Test as a normal user would use the CLI
 * Create a GitHub issue to reflect your contribution's background and reference it with Git commits

docs/usage.rst

@@ -87,7 +87,7 @@ Usage (Developers)
 
 Developers are free to use the user guide above to familiarize with the CLI and save time from having to install any dependencies, but development within a Conda environment is heavily recommended regardless
 
-Gain access to the repository with *git clone [email protected]:NOAA-GFDL/fre-cli.git* or your fork's link (recommended) and an SSH RSA key
+Gain access to the repository with *git clone --recursive [email protected]:NOAA-GFDL/fre-cli.git* or your fork's link (recommended) and an SSH RSA key
 
 Once inside the repository, developers can test local changes by running a *pip install .* inside of the root directory to install the fre-cli package locally with the newest local changes
 

fre/cmor/README.md

@@ -29,18 +29,39 @@ this subtool's help, and command-specific `run` help:
 
 
 # subtool command-specific help, e.g. for run
-> fre cmor run --help
-    Usage: fre cmor run [OPTIONS]
-
-      Rewrite climate model output
-
-    Options:
-      -d, --indir TEXT         Input directory  [required]
-      -l, --varlist TEXT       Variable list  [required]
-      -r, --table_config TEXT  Table configuration  [required]
-      -p, --exp_config TEXT    Experiment configuration  [required]
-      -o, --outdir TEXT        Output directory  [required]
-      --help                   Show this message and exit.
+> fre cmor run --help                        
+Usage: fre cmor run [OPTIONS]                                                 
+                                                                              
+  Rewrite climate model output files with CMIP-compliant metadata for down-   
+  stream publishing                                                           
+                                                                              
+Options:                                                                      
+  -d, --indir TEXT         directory containing netCDF files. keys specified  
+                           in json_var_list are local variable names used for 
+                           targeting specific files in this directory         
+                           [required]                                         
+  -l, --varlist TEXT       path pointing to a json file containing directory  
+                           of key/value pairs. the keys are the 'local' names 
+                           used in the filename, and the values pointed to by 
+                           those keys are strings representing the name of the
+                           variable contained in targeted files. the key and  
+                           value are often the same, but it is not required.  
+                           [required]                                         
+  -r, --table_config TEXT  json file containing CMIP-compliant per-           
+                           variable/metadata for specific MIP table. The MIP  
+                           table can generally be identified by the specific  
+                           filename (e.g. 'Omon')  [required]                 
+  -p, --exp_config TEXT    json file containing metadata dictionary for       
+                           CMORization. this metadata is effectively appended 
+                           to the final output file's header  [required]      
+  -o, --outdir TEXT        directory root that will contain the full output   
+                           and output directory structure generated by the    
+                           cmor module upon request.  [required]              
+  -v, --opt_var_name TEXT  optional, specify a variable name to specifically  
+                           process only filenames matching that variable name.
+                           I.e., this string help target local_vars, not      
+                           target_vars.                                       
+  --help                   Show this message and exit.                        
 ```