Create a new example that will run full ADF package (not from notebook)

cupid/build.py

@@ -16,6 +16,7 @@
 """
 from __future__ import annotations
 
+import shutil
 import subprocess
 
 import click
@@ -45,6 +46,14 @@ def build(config_path):
     subprocess.run(
         ["jupyter-book", "build", f"{run_dir}/computed_notebooks/{sname}", "--all"],
     )
+    adf_run = control["compute_notebooks"]["atm"]["link_to_ADF"]["parameter_groups"][
+        "none"
+    ]["adf_run"]
+    if adf_run:
+        shutil.copytree(
+            f"{run_dir}/ADF",
+            f"{run_dir}/computed_notebooks/{sname}/_build/html/ADF",
+        )
 
     # Originally used this code to copy jupyter book HTML to a location to host it online
 
@@ -59,3 +68,7 @@ def build(config_path):
     #                 f"{user}@{remote_mach}:{remote_dir}"])
 
     return None
+
+
+if __name__ == "__main__":
+    build()

examples/external_diag_packages/config.yml

@@ -0,0 +1,225 @@
+################## SETUP ##################
+
+################
+# Data Sources #
+################
+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: external_diag_packages
+
+    # run_dir is the path to the folder you want
+    ### all the files associated with this configuration
+    ### to be created in
+    run_dir: .
+
+    # nb_path_root is the path to the folder that cupid will
+    ### 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: ../nblibrary
+
+######################
+# Computation Config #
+######################
+
+computation_config:
+
+    # default_kernel_name is the name of the environment that
+    ### the notebooks in this configuration will be run in by default.
+    ### It must already be installed on your machine. You can also
+    ### specify a different environment than the default for any
+    ### notebook in NOTEBOOK CONFIG
+    default_kernel_name: cupid-analysis
+
+    # log level sets the level of how verbose logging will be.
+    # options include: debug, info, warning, error
+    log_level: 'info'
+
+############# NOTEBOOK CONFIG #############
+
+############################
+# Notebooks and Parameters #
+############################
+
+# All parameters under global_params get passed to all the notebooks
+
+global_params:
+  case_name: 'b.e30_beta02.BLT1850.ne30_t232.104'
+  base_case_name: 'f.e23_alpha17f.FLTHIST_ne30.roughtopo.099'
+  CESM_output_dir: /glade/campaign/cesm/development/cross-wg/diagnostic_framework/CESM_output_for_testing
+  start_date: '0001-01-01'
+  end_date: '0101-01-01'
+  lc_kwargs:
+    threads_per_worker: 1
+
+timeseries:
+  num_procs: 8
+  ts_done: [False, False]
+  overwrite_ts: [False, False]
+  case_name: ['b.e30_beta02.BLT1850.ne30_t232.104', 'f.e23_alpha17f.FLTHIST_ne30.roughtopo.099']
+
+  atm:
+    vars: ['PSL']
+    derive_vars: []
+    hist_str: 'h0a'
+    start_years: [1,1]
+    end_years: [100,100]
+    level: 'lev'
+
+  lnd:
+    vars: []
+    derive_vars: []
+    hist_str: 'h0'
+    start_years: [1,1]
+    end_years: [100,100]
+    level: 'lev'
+
+  ocn:
+    vars: []
+    derive_vars: []
+    hist_str: 'h.z'
+    start_years: [1,1]
+    end_years: [100,100]
+    level: 'lev'
+
+  ice:
+    vars: []
+    derive_vars: []
+    hist_str: 'h'
+    start_years: [1,1]
+    end_years: [100,100]
+    level: 'lev'
+
+  glc:
+    vars: []
+    derive_vars: []
+    hist_str: 'initial_hist'
+    start_years: [1,1]
+    end_years: [100,100]
+    level: 'lev'
+
+compute_notebooks:
+
+  # This is where all the notebooks you want run and their
+  # parameters are specified. Several examples of different
+  # types of notebooks are provided.
+
+  # The first key (here infrastructure) is the name of the
+  # notebook from nb_path_root, minus the .ipynb
+
+    infrastructure:
+      index:
+        parameter_groups:
+          none: {}
+
+    atm:
+      link_to_ADF:
+        kernel_name: cupid-dev
+        parameter_groups:
+          none:
+            adf_root: ../../external_diag_packages/ADF/
+            case_year_range: "1_100"
+            base_case_year_range: "1995_2006"
+        external_tool:
+          tool_name: 'ADF'
+          vars: ['PRECT', 'SST']
+          plotting_scripts: ["global_latlon_map", "global_latlon_vect_map"]
+
+#    glc:
+#      LIWG_SMB_diagnostic:
+#        parameter_groups:
+#          none:
+#            obs_path: '/glade/u/home/gunterl/obs_diagnostic_cesm/'
+#            obs_name: 'GrIS_MARv3.12_climo_1960_1999.nc'
+#            climo_nyears: 40
+
+#    ice:
+#      seaice:
+#        parameter_groups:
+#          none:
+#            cases:
+#              - g.e23_a16g.GJRAv4.TL319_t232_hycom1_N75.2024.005
+#              - g.e23_a16g.GJRAv4.TL319_t232_zstar_N65.2024.004
+#            begyr1: 245
+#            endyr1: 305
+#            begyr2: 245
+#            endyr2: 305
+#            nyears: 25
+
+#    lnd:
+#      land_comparison:
+#        parameter_groups:
+#          none:
+#            cases:
+#              - ctsm51d159_f45_GSWP3_bgccrop_1850pAD
+#              - ctsm51d159_f45_GSWP3_bgccrop_1850pSASU
+#            type:
+#              - 1850pAD
+#              - 1850pSASU
+
+#    ocn:
+#      ocean_surface:
+#        parameter_groups:
+#          none:
+#            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
+
+########### JUPYTER BOOK CONFIG ###########
+
+##################################
+# Jupyter Book Table of Contents #
+##################################
+book_toc:
+
+  # See https://jupyterbook.org/en/stable/structure/configure.html for
+  # complete documentation of Jupyter book construction options
+
+  format: jb-book
+
+  # All filenames are notebook filename without the .ipynb, similar to above
+
+  root: infrastructure/index # root is the notebook that will be the homepage for the book
+  parts:
+
+    # Parts group notebooks into different sections in the Jupyter book
+    # table of contents, so you can organize different parts of your project.
+    # Each chapter is the name of one of the notebooks that you executed
+    # in compute_notebooks above, also without .ipynb
+
+    - caption: Atmosphere
+      chapters:
+        - file: atm/link_to_ADF
+
+    # - caption: Ocean
+    #   chapters:
+    #       - file: ocn/ocean_surface
+
+    # - caption: Land
+    #   chapters:
+    #     - file: lnd/land_comparison
+
+    # - caption: Sea Ice
+    #   chapters:
+    #     - file: ice/seaice
+
+    # - caption: Land Ice
+    #   chapters:
+    #     - file: glc/LIWG_SMB_diagnostic
+
+#####################################
+# Keys for Jupyter Book _config.yml #
+#####################################
+book_config_keys:
+
+  title: External Diagnostic Packages  # Title of your jupyter book
+
+  # Other keys can be added here, see https://jupyterbook.org/en/stable/customize/config.html
+  ### for many more options