Merge pull request #32 from mnlevy1981/reorg_externals

Reorganize externals

.gitignore

@@ -11,3 +11,5 @@ nbscuid.egg-info
 
 # Text editor temp files
 **/*.swp
+
+externals/

Externals.cfg

@@ -1,9 +1,15 @@
-[nbscuid_adf_examples]
-local_path = examples/externals/
+[ADF]
+local_path = externals/ADF
 branch = main
 protocol = git
-repo_url = https://github.com/rmshkv/nbscuid-adf-sandbox.git
-sparse = ../.nblibrary_sparse_checkout
+repo_url = https://github.com/NCAR/ADF.git
+required = True
+
+[mom6-tools]
+local_path = externals/mom6-tools
+branch = main
+protocol = git
+repo_url = https://github.com/NCAR/mom6-tools.git
 required = True
 
 [externals_description]

README.md

@@ -18,7 +18,8 @@ CUPiD is a collaborative effort that unifies all CESM component diagnostics and
 To install CUPiD, you need to check out the code and then set up a few environments.
 The initial examples have hard-coded paths that require you to be on `casper`.
 
-The code relies on submodules to install `manage_externals` and then uses `manage_externals` for one more package, so the `git clone` process is a little more complicated than usual:
+The code relies on submodules to install `manage_externals` and then uses `manage_externals` for a few packages that are still being developed,
+so the `git clone` process is a little more complicated than usual:
 
 ```
 $ git clone --recurse-submodules https://github.com/NCAR/CUPiD.git
@@ -30,15 +31,16 @@ Then build the necessary conda environments with
 
 ```
 $ conda env create -f nbscuid/dev-environment.yml
+$ conda activate nbscuid-dev
 $ which nbscuid-run
 $ conda env create -f mom6-environment.yml
 ```
 
 Notes:
 
 1. `conda` now defaults to using `mamba` to solve environments; the `mom6-environment.yml` environment is complicated, so older versions of `conda` should be updated (`conda update -n base conda`) or you should use `mamba` instead.
-
-2. IF `which nbscuid-run` returned the error `which: no nbscuid-run in ($PATH)`, then please run the following:
+1. If `./manage_externals/checkout_externals` is not found, run `git submodule update --init` to clone the submodule.
+1. If `which nbscuid-run` returned the error `which: no nbscuid-run in ($PATH)`, then please run the following:
 
 ```
 $ conda activate nbscuid-dev

examples/adf-mom6/config.yml

@@ -19,7 +19,7 @@ data_sources:
     ### look for your template notebooks in. It doesn't have to 
     ### be inside run_dir, or be specific to this project, as
     ### long as the notebooks are there
-    nb_path_root: ../externals/nblibrary
+    nb_path_root: ../nblibrary
 
 ######################
 # Computation Config #
@@ -64,7 +64,7 @@ compute_notebooks:
     parameter_groups:
       none:
         sname: *sname
-        adf_path: ./ADF
+        adf_path: ../../externals/ADF
         config_path: .
         config_fil_str: "config_f.cam6_3_119.FLTHIST_ne30.r328_gamma0.33_soae.001.yaml"
 

examples/adf-only/config-adf-only.yml

@@ -19,7 +19,7 @@ data_sources:
     ### look for your template notebooks in. It doesn't have to 
     ### be inside run_dir, or be specific to this project, as
     ### long as the notebooks are there
-    nb_path_root: ../externals/nblibrary
+    nb_path_root: ../nblibrary
 
 ######################
 # Computation Config #
@@ -64,9 +64,9 @@ compute_notebooks:
     parameter_groups:
       none:
         sname: *sname
-        adf_path: ./ADF
+        adf_path: ../../externals/ADF
         config_path: .
-        config_fil_str: "config_f.cam6_3_119.FLTHIST_ne30.r328_gamma0.33_soae_numcin3.001_vs_f.cam6_3_119.FLTHIST_ne30.r328_gamma0.33_soae.001.yaml"
+        config_fil_str: "config_f.cam6_3_119.FLTHIST_ne30.r328_gamma0.33_soae.001.yaml"
 
 
 

examples/nblibrary/.gitignore

@@ -0,0 +1 @@
+PNG