Merge branch 'main' into 534_ao_extremes

.github/workflows/build_workflow.yml

@@ -9,6 +9,10 @@ on:
 
   workflow_dispatch:
 
+env:
+    CANCEL_OTHERS: true
+    PATHS_IGNORE: '["**/README.rst", "**/docs/**", "**/ISSUE_TEMPLATE/**", "**/pull_request_template.md", "**/.vscode/**"]'
+
 jobs:
   check-jobs-to-skip:
     runs-on: ubuntu-latest
@@ -27,25 +31,16 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 10
     steps:
-      - uses: actions/setup-node@v3
-        with:
-          node-version: '16'
       - name: Checkout Code Repository
         uses: actions/checkout@v3
-        with:
-          node-version: '16'
+
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          node-version: '16'
           python-version: '3.10'
-      # Run all pre-commit hooks on all the files.
-      # Getting only staged files can be tricky in case a new PR is opened
-      # since the action is run on a branch in detached head state
+
       - name: Install and Run Pre-commit
         uses: pre-commit/action@v3.0.0
-        with:
-          node-version: '16'
 
   build:
     needs: check-jobs-to-skip
@@ -56,9 +51,6 @@ jobs:
         shell: bash -l {0}
     timeout-minutes: 10
     steps:
-      - uses: actions/setup-node@v3
-        with:
-          node-version: '16'
       - uses: actions/checkout@v3
 
       - name: Set up Conda Environment
@@ -82,7 +74,6 @@ jobs:
       - name: Cache Conda
         uses: actions/cache@v3
         with:
-          node-version: '16'
           path: ${{ env.CONDA }}/envs
           key:
             conda-${{ runner.os }}--${{ runner.arch }}--${{

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 # Configuration file for `pre-commit` tool.
 # Source: https://pre-commit.com/#pre-commit-configyaml---top-level
-exclude: "docs|node_modules|migrations|.git|.tox|.md|sample_setups/(external-setups|jsons)|tests/deprecated"
+exclude: "docs|node_modules|migrations|.git|.tox|README.md|sample_setups/(external-setups|jsons)|tests/deprecated"
 default_stages: [commit]
 fail_fast: true
 
@@ -20,16 +20,15 @@ repos:
     # Python code formatters
     # =======================
     - repo: https://github.com/psf/black
-      rev: 23.1.0
+      rev: 23.3.0
       hooks:
           - id: black
 
-    - repo: https://github.com/PyCQA/isort
+    - repo: https://github.com/timothycrosley/isort
       rev: 5.12.0
       hooks:
           - id: isort
 
-
     # =======================
     # Python linting
     # =======================

docs/index.rst

@@ -16,10 +16,11 @@ regional monsoons, and high frequency characteristics of simulated precipitation
 
 `PCMDI`_ uses the PMP to produce `quick-look simulation summaries across generations of CMIP <https://pcmdi.llnl.gov/metrics>`_.
 
-The PMP expects model data to be `CF-compliant <http://cfconventions.org/>`_, otherwise, 
-to successfully use the package may require some input data conditioning. 
-It is also strongly suggested to work with observation datasets following the `CF-compliant <http://cfconventions.org/>`_, 
-such as datasets from the `obs4MIPs`_ project. 
+.. raw:: html
+
+    <div style="position: relative; padding-bottom: 56.25%; height: 0; overflow: hidden; max-width: 80%; height: auto; margin-left: auto; margin-right: auto">
+        <iframe src="https://www.youtube.com/embed/STfCq5Biqf0" frameborder="0" allowfullscreen style="position: absolute; top: 0; left: 0; width: 100%; height: 100%;"></iframe>
+    </div>
 
 
 Getting Started
@@ -31,6 +32,16 @@ are summarized with interactive Jupyter notebooks in the :ref:`metrics` page
 
 Some installation support for CMIP participating modeling groups is available: pcmdi-metrics@llnl.gov
 
+The PMP expects model data to be `CF-compliant <http://cfconventions.org/>`_, otherwise, 
+to successfully use the package may require some input data conditioning. 
+It is also strongly suggested to work with observation datasets following the `CF-compliant <http://cfconventions.org/>`_, 
+such as datasets from the `obs4MIPs`_ project. 
+
+References
+==========
+Lee et al. (in prep, to be submitted soon), Objective Evaluation of Earth System Models: PCMDI Metrics Package (PMP) version 3, Geoscientific Model Development
+
+Gleckler et al. (2016), A more powerful reality test for climate models, Eos, 97, `doi:10.1029/2016EO051663 <https://eos.org/science-updates/a-more-powerful-reality-test-for-climate-models>`_.
 
 Acknowledgement
 ===============

docs/overview.rst

@@ -9,6 +9,12 @@ The primary application of the PMP is to evaluate simulations from the `Coupled
 It can also be used to provide objective performance summaries during the model development process as well as selected research purposes.  
 The notes below provide a brief summary of some of the key aspects of the PMP design.  
 
+.. raw:: html
+
+    <div style="position: relative; padding-bottom: 56.25%; height: 0; overflow: hidden; max-width: 80%; height: auto; margin-left: auto; margin-right: auto">
+        <iframe src="https://www.youtube.com/embed/STfCq5Biqf0" frameborder="0" allowfullscreen style="position: absolute; top: 0; left: 0; width: 100%; height: 100%;"></iframe>
+    </div>
+
 Software framework and dependencies
 -----------------------------------
 

docs/team.rst

@@ -15,4 +15,4 @@ Core developers
 * Peter Gleckler (LLNL)
 * Min-Seop Ahn (NASA)
 
-pcmdi-metrics@llnl.gov
+Contact: pcmdi-metrics@llnl.gov

pcmdi_metrics/cloud_feedback/cloud_feedback_driver.py

@@ -25,7 +25,6 @@
 version = param.version
 input_files_json = param.input_files_json
 path = param.path
-xml_path = param.xml_path
 data_path = param.data_path
 figure_path = param.figure_path
 output_path = param.output_path
@@ -45,7 +44,6 @@
 print("version:", version)
 print("path:", path)
 print("input_files_json:", input_files_json)
-print("xml_path:", xml_path)
 print("figure_path:", figure_path)
 print("output_path:", output_path)
 print("output_json_filename:", output_json_filename)
@@ -57,9 +55,6 @@
 else:
     exps = ["amip", "amip-p4K"]
 
-# generate xmls pointing to the cmorized netcdf files
-os.makedirs(xml_path, exist_ok=True)
-
 filenames = dict()
 
 if input_files_json is not None:
@@ -108,9 +103,7 @@
             searchstring = os.path.join(
                 ncfiles[exp][field]["path"], ncfiles[exp][field]["file"]
             )
-        xmlname = os.path.join(xml_path, ".".join([exp, model, variant, field, "xml"]))
-        os.system("cdscan -x " + xmlname + " " + searchstring)
-        filenames[exp][field] = xmlname
+        filenames[exp][field] = searchstring
 
 if debug:
     with open(os.path.join(output_path, "filenames.json"), "w") as f:
@@ -123,17 +116,17 @@
 
 # add this model's results to the pre-existing json file containing other models' results:
 updated_fbk_dict, updated_obsc_fbk_dict = organize_fbk_jsons(
-    fbk_dict, obsc_fbk_dict, model, variant, datadir=data_path
+    fbk_dict, obsc_fbk_dict, model, variant
 )
-updated_err_dict = organize_err_jsons(err_dict, model, variant, datadir=data_path)
+updated_err_dict = organize_err_jsons(err_dict, model, variant)
 
 ecs = None
 if get_ecs:
     # calculate ECS and add it to the pre-existing json file containing other models' results:
     ecs = compute_ECS(filenames)
     print("calc ECS done")
     print("ecs: ", ecs)
-updated_ecs_dict = organize_ecs_jsons(ecs, model, variant, datadir=data_path)
+updated_ecs_dict = organize_ecs_jsons(ecs, model, variant)
 
 os.makedirs(output_path, exist_ok=True)
 if debug: