Merge pull request NCAR#153 from TeaganKing/cleanup_1

Cleanup PR NCAR#1

NCARtips.md

@@ -38,5 +38,5 @@ and can be accessed via the following steps:
 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. In the terminal, run `cd ${CUPID_ROOT}/examples/key_metrics/computed_notebooks/_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.

README.md

@@ -53,18 +53,18 @@ please see the [Contributor's Guide](https://ncar.github.io/CUPiD/contributors_g
 ## Running
 
 CUPiD currently provides an example for generating diagnostics.
-To test the package out, try to run `examples/coupled-model`:
+To test the package out, try to run `examples/key-metrics`:
 
 ``` bash
 $ conda activate cupid-dev
-$ cd examples/coupled_model
+$ cd examples/key_metrics
 $ # machine-dependent: request multiple compute cores
 $ cupid-run
 $ cupid-build  # Will build HTML from Jupyter Book
 ```
 
-After the last step is finished, you can use Jupyter to view generated notebooks in `${CUPID_ROOT}/examples/coupled-model/computed_notebooks/quick-run`
-or you can view `${CUPID_ROOT}/examples/coupled-model/computed_notebooks/quick-run/_build/html/index.html` in a web browser.
+After the last step is finished, you can use Jupyter to view generated notebooks in `${CUPID_ROOT}/examples/key-metrics/computed_notebooks`
+or you can view `${CUPID_ROOT}/examples/key-metrics/computed_notebooks/_build/html/index.html` in a web browser.
 
 Notes:
 

cupid/build.py

@@ -39,12 +39,11 @@ def build(config_path):
     with open(config_path) as fid:
         control = yaml.safe_load(fid)
 
-    sname = control["data_sources"]["sname"]
     run_dir = control["data_sources"]["run_dir"]
 
-    subprocess.run(["jupyter-book", "clean", f"{run_dir}/computed_notebooks/{sname}"])
+    subprocess.run(["jupyter-book", "clean", f"{run_dir}/computed_notebooks"])
     subprocess.run(
-        ["jupyter-book", "build", f"{run_dir}/computed_notebooks/{sname}", "--all"],
+        ["jupyter-book", "build", f"{run_dir}/computed_notebooks", "--all"],
     )
     for component in control["compute_notebooks"]:
         for notebook in control["compute_notebooks"][component]:
@@ -57,7 +56,7 @@ def build(config_path):
                 ):
                     shutil.copytree(
                         f"{run_dir}/ADF_output",
-                        f"{run_dir}/computed_notebooks/{sname}/_build/html/ADF",
+                        f"{run_dir}/computed_notebooks/_build/html/ADF",
                     )
 
     # Originally used this code to copy jupyter book HTML to a location to host it online
@@ -69,7 +68,7 @@ def build(config_path):
     #         remote_dir = control["publish_location"]["remote_dir"]
     # this seems more complicated than expected...people have mentioned paramiko library?
     # subprocess.run(["mkdir", "-p", remote_dir])
-    # subprocess.run(["scp", "-r", f"{run_dir}/computed_notebooks/{sname}/_build/html/*",
+    # subprocess.run(["scp", "-r", f"{run_dir}/computed_notebooks/_build/html/*",
     #                 f"{user}@{remote_mach}:{remote_dir}"])
 
     return None

cupid/run.py

@@ -192,7 +192,7 @@ def run(
     # Grab paths
 
     run_dir = os.path.realpath(os.path.expanduser(control["data_sources"]["run_dir"]))
-    output_dir = run_dir + "/computed_notebooks/" + control["data_sources"]["sname"]
+    output_dir = run_dir + "/computed_notebooks/"
     temp_data_path = run_dir + "/temp_data"
     nb_path_root = os.path.realpath(
         os.path.expanduser(control["data_sources"]["nb_path_root"]),

cupid/util.py

@@ -141,7 +141,7 @@ def setup_book(config_path):
 
     os.makedirs(output_root, exist_ok=True)
 
-    output_dir = f'{output_root}/{control["data_sources"]["sname"]}'
+    output_dir = f"{output_root}"
 
     os.makedirs(output_dir, exist_ok=True)
 

docs/addingnotebookstocollection.md

@@ -6,7 +6,6 @@ Generally, a good fit for a diagnostic notebook is one that reads in CESM output
 1. Install the `environments/cupid-analysis.yml` environment (see [installation instructions](https://ncar.github.io/CUPiD/index.html#installing)). Make sure that your notebook runs properly in this environment. If there are conflicts or missing dependencies, open an issue or talk to CUPiD developers so we can find a solution.
 2. In your notebook, move all variables you might want to change (paths to data, dates to select, etc.) to a cell near the top. For example:
 
-            sname = "run_name"
             data_path = "path/to/data"
             dates = {"start_date" = "01/01/01",
                                     "end_date" = "01/01/02"}
@@ -15,7 +14,7 @@ Generally, a good fit for a diagnostic notebook is one that reads in CESM output
 ---
 **If you want to run your notebook through the `CUPiD` workflow yourself, follow the rest of the instructions:**
 
-4. Move your new diagnostic notebook to the folder called `examples/nblibrary`.
+4. Move your new diagnostic notebook to the folder called `nblibrary`.
 
 5. Open `config.yml`. First, add your new notebook (as its name, minus the `.ipynb`) to the list of notebooks that will be computed (`compute_notebooks`). The notebooks will be executed in the order they are listed here. For example:
 

docs/config.md

@@ -5,8 +5,6 @@ This page describes the fields in the configuration file that might commonly be
 <img src="_static/images/config/config_1.png" alt="CUPiD Config 1" width=1000 />
 The data sources section of the configuration file describes general data sources and expected directory structure for running CUPiD.
 
-`sname`: nickname for this configuration as a string. This will be used as the name of the folder your computed notebooks are put in
-
 <img src="_static/images/config/config_2.png" alt="CUPiD Config 2" width=1000 />
 The computation config section of the configuration file supplies the default kernel for running CUPiD. This should usually be `cupid-analysis`. If a contributor wants to include additional packages, please create an issue describing the packages you'd like to add to this conda environment.
 

examples/coupled_model/config.yml

@@ -4,10 +4,6 @@
 # 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: quick-run
-
     # run_dir is the path to the folder you want
     ### all the files associated with this configuration
     ### to be created in
@@ -17,7 +13,7 @@ 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: ../nblibrary
+    nb_path_root: ../../nblibrary
 
 ######################
 # Computation Config #

examples/external_diag_packages/config.yml

@@ -4,10 +4,6 @@
 # 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
@@ -17,7 +13,7 @@ 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: ../nblibrary
+    nb_path_root: ../../nblibrary
 
 ######################
 # Computation Config #
@@ -118,7 +114,7 @@ compute_notebooks:
         kernel_name: cupid-dev
         parameter_groups:
           none:
-            adf_root: ../../external_diag_packages/ADF/
+            adf_root: ../../examples/external_diag_packages/ADF_output/
             case_year_range: "1_100"
             base_case_year_range: "1995_2006"
         external_tool:

examples/key_metrics/config.yml

@@ -4,10 +4,6 @@
 # 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: key_metrics
-
     # run_dir is the path to the folder you want
     ### all the files associated with this configuration
     ### to be created in
@@ -17,7 +13,7 @@ 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: ../nblibrary
+    nb_path_root: ../../nblibrary
 
 ######################
 # Computation Config #
@@ -129,23 +125,23 @@ compute_notebooks:
             obs_name: 'GrIS_MARv3.12_climo_1960_1999.nc'
             climo_nyears: 40
 
-    rof:
-      global_discharge_gauge_compare_obs:
-        parameter_groups:
-          none:
-            analysis_name: ""
-            grid_name: 'f09_f09_mosart' # ROF grid name
-            rof_start_date: '0091-01-01'
-            rof_end_date: '0101-01-01'
-            figureSave: False
-      global_discharge_ocean_compare_obs:
-        parameter_groups:
-          none:
-            analysis_name: ""
-            grid_name: 'f09_f09_mosart' # ROF grid name
-            rof_start_date: '0091-01-01'
-            rof_end_date: '0101-01-01'
-            figureSave: False
+#    rof:
+#      global_discharge_gauge_compare_obs:
+#        parameter_groups:
+#          none:
+#            analysis_name: ""
+#            grid_name: 'f09_f09_mosart' # ROF grid name
+#            rof_start_date: '0091-01-01'
+#            rof_end_date: '0101-01-01'
+#            figureSave: False
+#      global_discharge_ocean_compare_obs:
+#        parameter_groups:
+#          none:
+#            analysis_name: ""
+#            grid_name: 'f09_f09_mosart' # ROF grid name
+#            rof_start_date: '0091-01-01'
+#            rof_end_date: '0101-01-01'
+#            figureSave: False
 
 #    ice:
 #      seaice:

helper_scripts/generate_adf_config_file.py

@@ -58,7 +58,7 @@ def generate_adf_config(cesm_root, cupid_example, adf_file, out_file):
     valid_examples = [
         example
         for example in next(os.walk(cupid_examples))[1]
-        if example not in ["ilamb", "nblibrary"]
+        if example not in ["ilamb"]
     ]
     if cupid_example not in valid_examples:
         error_msg = f"argument --cupid-example: invalid choice '{cupid_example}'"

helper_scripts/generate_cupid_config_for_cesm_case.py

@@ -95,7 +95,7 @@ def generate_cupid_config(case_root, cesm_root, cupid_example):
     valid_examples = [
         example
         for example in next(os.walk(cupid_examples))[1]
-        if example not in ["ilamb", "nblibrary"]
+        if example not in ["ilamb"]
     ]
     if cupid_example not in valid_examples:
         error_msg = f"argument --cupid-example: invalid choice '{cupid_example}'"

examples/nblibrary/atm/link_to_ADF.ipynb → nblibrary/atm/link_to_ADF.ipynb

@@ -61,7 +61,7 @@
     "base_case_name = None\n",
     "case_year_range = None\n",
     "base_case_year_range = None\n",
-    "# adf_root will be external_diag_packages/computed_notebooks/external_diag_packages/ADF/"
+    "# adf_root will be external_diag_packages/computed_notebooks/ADF/"
    ]
   },
   {