Merge branch 'MPAS-Dev/develop' into master

* MPAS-Dev/MPAS-Analysis/develop: (122 commits)
  Keep Time dim sorted during time series caching
  Check totalDays and totalMonths in clim. unit test
  Fix the month masking for climatology caching
  Adds author information to functions
  Remove cached files if they get corrupted
  Add unit test for cache_climatologies
  Break cache_climatology into 3 helper functions
  Add namelistMaps
  Add find_option to Namelist
  Fix args to _compute_moc_time_series_part
  Add comment about MOC maxChunkSize to config.default
  Modifies doc-strings
  Improved climatology for performance
  Adds chunking for problematic edison moc case
  Adds observation panels to Nino diagnostics
  Cleans up chunking via custom chunking
  Tests casting for config parser `getExpression`
  Returns `None` for empty config option
  Improve docstring on maskVaries in climatology
  Switch to make_directories
  ...

.gitignore

@@ -1,6 +1,6 @@
 # User defined config files
-/config.analysis.*
-/config.analysis_*
+/config.*
+!/config.default
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

README.md

@@ -12,19 +12,44 @@ This analysis repository presumes that the following python packages are availab
  * numpy
  * scipy
  * matplotlib
- * numexpr
- * ipython-notebook
  * netCDF4
- * progressbar
- * vtk
- * pyevtk with `conda install -c https://conda.anaconda.org/opengeostat pyevtk`
- * cartopy with `conda install -c scitools cartopy`
- * xarray
+ * xarray ≥ 0.9.1
  * dask
  * bottleneck
+ * basemap
+ * lxml
+ * nco
 
 You can easily install them via the conda command:
 
 ```
-conda install -c scitools  -c https://conda.anaconda.org/opengeostat numpy scipy matplotlib ipython notebook netCDF4 progressbar vtk cartopy xarray dask bottleneck pyevtk numexpr
+conda config --add channels conda-forge
+conda install numpy scipy matplotlib netCDF4 xarray dask bottleneck basemap lxml nco
 ```
+
+## Running the analysis
+  1. Create and empty config file (say `config.myrun`) or copy one of the
+     example files in the `configs` directory.
+  2. Copy and modify any config options you want to change from
+     `config.default` into your new config file.
+
+     **Requirements for custom config files:**
+     * At minimum you should set `baseDirectory` under `[output]` to the folder
+       where output is stored.  **NOTE** this value should be a unique
+       directory for each run being analyzed.  If multiple runs are analyzed in
+       the same directory, cached results from a previous analysis will not be
+       updated correctly.
+     * Any options you copy into the config file **must** include the
+       appropriate section header (e.g. '[run]' or '[output]')
+     * The entire `config.default` does not need to be used.  This fill will
+       automatically be used for any options you do not include in your custom
+       config file.
+     * Given the automatic sourcing of `config.default` you should **not**
+       alter `config.default` directly.
+  3. run: `./run_analysis.py config.myrun`.  This will read the configuraiton
+     first from `config.default` and then replace that configuraiton with any
+     changes from from `config.myrun`
+  4. If you want to run a subset of the analysis, you can either set the
+     `generate` option under `[output]` in your config file or use the
+     `--generate` flag on the command line.  See the comments in
+     `config.default` for more details on this option.

ci/requirements-py27.yml

@@ -1,4 +1,6 @@
 name: test_env
+channels:
+  - conda-forge
 dependencies:
   - python=2.7
   - pytest
@@ -8,3 +10,7 @@ dependencies:
   - xarray
   - matplotlib
   - dask
+  - netcdf4
+  - hdf5
+  - hdf4
+  - nco