Merge pull request #55 from mnlevy1981/pass_paths_via_config

Pass paths via config

README.md

@@ -66,10 +66,13 @@ After the last step is finished, you can use Jupyter to view generated notebooks
 or you can copy the entire `${CUPID_ROOT}/examples/coupled-model/computed_notebooks/quick-run/_build/html`
 directory to your local machine and look at `index.html` in a web browser.
 
-For users running on the NCAR super computers (derecho or casper), you can visualize the web page in a browser with the following steps:
-1. open a new browser window that points to https://fastx.ucar.edu:3300/session/
-1. open a default desktop icon
-1. select the browser client
-1. type `xterm` and hit enter to open a terminal
-1. In the terminal, run `cd ${CUPID_ROOT}/examples/coupled_model/computed_notebooks/quick-run/_build/html` to enter the `html` directory
-1. From the updated directory, run `firefox index.html &` to open a web browser pointed at the generated web page
+### Looking at Output
+
+For users running on the NCAR super computers (derecho or casper), you can visualize the web page in a browser using the FastX service. FastX requires you to be on the internal NCAR network (either on-site or via the VPN, and can be accessed via the following steps:
+
+1. Open a new browser window that points to https://fastx.ucar.edu:3300/session/
+1. Open a default desktop icon.
+1. Select the browser client.
+1. Type `xterm` and hit enter to open a terminal.
+1. In the terminal, run `cd ${CUPID_ROOT}/examples/coupled_model/computed_notebooks/quick-run/_build/html` to enter the `html` directory.
+1. From the updated directory, run `firefox index.html &` to open a web browser pointed at the generated web page.

cupid/run.py

@@ -71,7 +71,7 @@ def run():
     #####################################################################
     # Ploomber - making a DAG
 
-    dag = ploomber.DAG(executor=ploomber.executors.Parallel())
+    dag = ploomber.DAG(executor=ploomber.executors.Serial())
 
 
     #####################################################################

examples/coupled_model/config.yml

@@ -7,8 +7,7 @@
 data_sources:
     # sname is any string used as a nickname for this configuration. It will be
     ### used as the name of the folder your computed notebooks are put in
-    sname: &sname
-      quick-run
+    sname: quick-run
 
     # run_dir is the path to the folder you want
     ### all the files associated with this configuration
@@ -45,7 +44,7 @@ computation_config:
 # All parameters under global_params get passed to all the notebooks
 
 global_params:
-    test_global_param: hello
+  CESM_output_dir: /glade/campaign/cesm/development/cross-wg/diagnostic_framework/CESM_output_for_testing
 
 compute_notebooks:
 
@@ -57,27 +56,39 @@ compute_notebooks:
   ### notebook from nb_path_root, minus the .ipynb
   index:
     parameter_groups:
-      none:
-        sname: *sname
+      none: {}
 
   adf_quick_run:
     parameter_groups:
       none:
-        sname: *sname
         adf_path: ../../externals/ADF
         config_path: .
         config_fil_str: "config_f.cam6_3_119.FLTHIST_ne30.r328_gamma0.33_soae.001.yaml"
 
-  surface:
+  ocean_surface:
     parameter_groups:
       none:
-        sname: *sname
+        Case: b.e23_alpha16b.BLT1850.ne30_t232.054
+        savefigs: False
+        mom6_tools_config:
+          start_date: '0091-01-01'
+          end_date: '0101-01-01'
+          Fnames:
+            native: 'mom6.h.native.????-??.nc'
+            static: 'mom6.h.static.nc'
+          oce_cat: /glade/u/home/gmarques/libs/oce-catalogs/reference-datasets.yml
+
 
 
-  land_comparision:
+  land_comparison:
     parameter_groups:
       none:
-        sname: *sname
+        cases:
+          - ctsm51d159_f45_GSWP3_bgccrop_1850pAD
+          - ctsm51d159_f45_GSWP3_bgccrop_1850pSASU
+        type:
+          - 1850pAD
+          - 1850pSASU
 
 
 ########### JUPYTER BOOK CONFIG ###########
@@ -109,11 +120,11 @@ book_toc:
 
     - caption: Ocean
       chapters:
-          - file: surface
+          - file: ocean_surface
 
     - caption: Land
       chapters:
-        - file: land_comparision
+        - file: land_comparison
 
 #####################################
 # Keys for Jupyter Book _config.yml #

examples/nblibrary/adf_quick_run.ipynb

@@ -788,7 +788,6 @@
     "import matplotlib.pyplot as plt\n",
     "import xarray as xr\n",
     "import numpy as np\n",
-    "import matplotlib.ticker as ticker\n",
     "from matplotlib.ticker import MultipleLocator\n",
     "from matplotlib.lines import Line2D\n",
     "\n",