Merge branch 'develop' into cli-ish

.github/workflows/ci.yml

@@ -30,9 +30,6 @@ jobs:
           extra-specs: |
             pytest
 
-      - name: Install MM
-        run: python -m pip install -e . --no-deps -v
-
       - if: ${{ matrix.monet == 'dev' }}
         name: Install development versions of monet and monetio
         run: |
@@ -49,7 +46,7 @@ jobs:
           python -c "import monet;   print('monet.__version__',   getattr(monet, '__version__', '?'))"
 
       - name: pytest
-        run: python -m pytest melodies_monet
+        run: python -m pytest -v melodies_monet
 
       - name: Run docs/examples notebooks as scripts
         run: |
@@ -62,12 +59,33 @@ jobs:
           done
           cd -
 
+      - name: Prepare idealized save/read cases
+        shell: python
+        run: |
+          from copy import deepcopy
+          import yaml
+
+          with open('docs/examples/control_idealized.yaml') as f:
+            ctl = yaml.safe_load(f)
+          assert {'save', 'read'} < ctl['analysis'].keys()
+
+          ctl_save = deepcopy(ctl)
+          del ctl_save['analysis']['read']
+          with open('docs/examples/control_idealized_save.yaml', 'w') as f:
+            yaml.safe_dump(ctl_save, f)
+
+          ctl_read = deepcopy(ctl)
+          del ctl_read['analysis']['save']
+          with open('docs/examples/control_idealized_read.yaml', 'w') as f:
+            yaml.safe_dump(ctl_read, f)
+
       - name: Check CLI works
         run: |
           cd docs/examples
           melodies-monet --version
           python -m melodies_monet --version
-          melodies-monet run control_idealized.yaml
+          melodies-monet run control_idealized_save.yaml
+          melodies-monet run control_idealized_read.yaml
           cd -
 
   docs:
@@ -81,7 +99,7 @@ jobs:
       - uses: actions/checkout@v3
 
       - name: Set up Python (micromamba)
-        uses: mamba-org/provision-with-micromamba@v12
+        uses: mamba-org/provision-with-micromamba@v15
         with:
           environment-file: docs/environment-docs.yml
           cache-env: true

docs/appendix/yaml.rst

@@ -106,6 +106,10 @@ data (e.g., surf_only: True).
 Typically this is set at the horizontal resolution of your model * 1.5. Setting 
 this to a smaller value will speed up the pairing process. 
 
+**apply_ak:** This is an optional argument used for pairing of satellite data. This
+should be set to True when application of satellite averaging kernels or apriori data 
+to model observations is desired. 
+
 **mapping:** This is the mapping dictionary for all variables to be plotted. 
 For each observational dataset, add a mapping dictionary where the model 
 variable name is first (i.e., key) and the observation variable name is second 
@@ -362,8 +366,8 @@ observation label is first and the model label is second
      used for averaging and plotting. Options are 'time' for UTC or 'time_local' 
      for local time
    * **ts_avg_window:** This is for timeseries plots only. This is the averaging 
-     window applied to the data. Options are None for no averaging or a pandas 
-     resample rule (e.g., 'H' is hourly, 'D' is daily).
+     window applied to the data. No averaging done if not provided in the yaml file (i.e., ts_avg_window is optional). Averaging is done if a pandas 
+     resample rule (e.g., 'H' is hourly, 'D' is daily) is specified.
 
 Stats
 -----

docs/background/gridded_datasets.rst

@@ -0,0 +1,5 @@
+Gridded Datasets
+================
+
+Gridded datasets
+

docs/background/time_chunking.rst

@@ -0,0 +1,5 @@
+Time Chunking
+================
+
+Time chunking
+

docs/conf.py

@@ -199,6 +199,7 @@
     # Sphinx 4.5 linkcheck having problem:
     "https://docs.github.com/en/authentication/connecting-to-github-with-ssh/adding-a-new-ssh-key-to-your-github-account",
 ]
+user_agent = "Mozilla/5.0 (X11; Linux x86_64; rv:25.0) Gecko/20100101 Firefox/25.0"
 
 autosectionlabel_prefix_document = True
 autosectionlabel_maxdepth = 2

docs/develop/developers_guide.rst

@@ -74,7 +74,7 @@ these instructions:
 
        $ conda create --name melodies-monet python=3.9
        $ conda activate melodies-monet
-       $ conda install -y -c conda-forge pyyaml monet monetio netcdf4 wrf-python typer rich pooch jupyterlab
+       $ conda install -y -c conda-forge pyyaml pandas=1 monet monetio netcdf4 wrf-python typer rich pooch jupyterlab
 
 (b) Clone [#clone]_ and link the latest development versions of MONET and MONETIO from GitHub to
     your conda environment::

docs/environment-docs.yml

@@ -12,6 +12,7 @@ dependencies:
   - netcdf4
   - numpy
   - pandas<2
+  - pillow<10
   #
   # Extras
   - pooch

docs/index.rst

@@ -47,6 +47,8 @@ MONETIO please refer to:
    background/supported_analyses
    background/supported_plots
    background/supported_stats
+   background/time_chunking
+   background/gridded_datasets
 
 .. toctree::
    :hidden:

docs/tutorial/installation.rst

@@ -34,7 +34,7 @@ First create and activate a conda environment::
 
 Add dependencies from conda-forge::
 
-    $ conda install -y -c conda-forge pyyaml monet monetio netcdf4 wrf-python typer rich pooch
+    $ conda install -y -c conda-forge pyyaml pandas=1 monet monetio netcdf4 wrf-python typer rich pooch
 
 Now, install the stable branch of MELODIES MONET to the environment::