Add instructions for setting ESMFMKFILE and update links to xESMF d…

…ocs (#643)

README.rst

@@ -182,7 +182,7 @@ Things We Are Striving For
 * Support for parallelism using `dask`_ where it is both possible and makes sense
 
 .. _Metadata Interpretation: https://xcdat.readthedocs.io/en/stable/faqs.html#metadata-interpretation
-.. _xESMF: https://pangeo-xesmf.readthedocs.io/en/latest/
+.. _xESMF: https://xesmf.readthedocs.io/en/latest/
 .. _regrid2: https://cdms.readthedocs.io/en/latest/regrid2.html
 .. _xgcm: https://xgcm.readthedocs.io/en/latest/index.html
 .. _dask: https://dask.org/

docs/examples/regridding-horizontal.ipynb

@@ -17,7 +17,10 @@
     "\n",
     "- [xarray.Dataset.regridder.horizontal](../generated/xarray.Dataset.regridder.horizontal.rst)\n",
     "\n",
-    "The data used in this example can be found through the [Earth System Grid Federation (ESGF) search portal](https://aims2.llnl.gov/search).\n",
+    "## Other Resources\n",
+    "\n",
+    "- [xESMF documentation](https://xesmf.readthedocs.io/en/latest/)\n",
+    "- The data used in this example can be found through the [Earth System Grid Federation (ESGF) search portal](https://aims2.llnl.gov/search).\n",
     "\n",
     "## Overview\n",
     "\n",
@@ -653,7 +656,7 @@
     "# Unit adjust (-273.15, K to C)\n",
     "ds[\"tas\"] = ds[\"tas\"] - 273.15\n",
     "\n",
-    "ds\n"
+    "ds"
    ]
   },
   {
@@ -751,10 +754,12 @@
     "\n",
     "fig, axes = plt.subplots(ncols=2, figsize=(16, 4))\n",
     "\n",
-    "ds.tas.isel(time=0).plot(ax=axes[0], vmin=-40, vmax=40, extend='both', cmap = 'RdBu_r')\n",
+    "ds.tas.isel(time=0).plot(ax=axes[0], vmin=-40, vmax=40, extend=\"both\", cmap=\"RdBu_r\")\n",
     "axes[0].set_title(\"Input data\")\n",
     "\n",
-    "output.tas.isel(time=0).plot(ax=axes[1], vmin=-40, vmax=40, extend='both', cmap = 'RdBu_r')\n",
+    "output.tas.isel(time=0).plot(\n",
+    "    ax=axes[1], vmin=-40, vmax=40, extend=\"both\", cmap=\"RdBu_r\"\n",
+    ")\n",
     "axes[1].set_title(\"Output data\")\n",
     "\n",
     "plt.tight_layout()"
@@ -771,7 +776,7 @@
     "\n",
     "In this example, we will compare the different regridding methods supported by `xESMF`.\n",
     "\n",
-    "You can find a more in depth comparison on `xESMF`'s [documentation](https://pangeo-xesmf.readthedocs.io/en/latest/notebooks/Compare_algorithms.html).\n",
+    "You can find a more in depth comparison on `xESMF`'s [documentation](https://xesmf.readthedocs.io/en/latest/notebooks/Compare_algorithms.html).\n",
     "\n",
     "Methods:\n",
     "\n",
@@ -809,7 +814,9 @@
     "for i, method in enumerate(methods):\n",
     "    output = ds.regridder.horizontal(\"tas\", output_grid, tool=\"xesmf\", method=method)\n",
     "\n",
-    "    output.tas.isel(time=0).plot(ax=axes[i], vmin=-40, vmax=40, extend='both', cmap = 'RdBu_r')\n",
+    "    output.tas.isel(time=0).plot(\n",
+    "        ax=axes[i], vmin=-40, vmax=40, extend=\"both\", cmap=\"RdBu_r\"\n",
+    "    )\n",
     "\n",
     "    axes[i].set_title(method)\n",
     "\n",
@@ -861,7 +868,9 @@
     "ds[\"mask\"].plot(ax=axes[0], cmap=\"binary_r\")\n",
     "axes[0].set_title(\"Mask\")\n",
     "\n",
-    "masked_output.tas.isel(time=0).plot(ax=axes[1], vmin=-40, vmax=40, extend='both', cmap='RdBu_r')\n",
+    "masked_output.tas.isel(time=0).plot(\n",
+    "    ax=axes[1], vmin=-40, vmax=40, extend=\"both\", cmap=\"RdBu_r\"\n",
+    ")\n",
     "axes[1].set_title(\"Masked output\")\n",
     "\n",
     "plt.tight_layout()"
@@ -915,9 +924,11 @@
     "\n",
     "fig, axes = plt.subplots(ncols=2, figsize=(16, 4))\n",
     "\n",
-    "ds.tas.isel(time=0).plot(ax=axes[0], vmin=-40, vmax=40, extend='both', cmap = 'RdBu_r')\n",
+    "ds.tas.isel(time=0).plot(ax=axes[0], vmin=-40, vmax=40, extend=\"both\", cmap=\"RdBu_r\")\n",
     "\n",
-    "output.tas.isel(time=0).plot(ax=axes[1], vmin=-40, vmax=40, extend='both', cmap = 'RdBu_r')"
+    "output.tas.isel(time=0).plot(\n",
+    "    ax=axes[1], vmin=-40, vmax=40, extend=\"both\", cmap=\"RdBu_r\"\n",
+    ")"
    ]
   }
  ],

docs/getting-started-guide/installation.rst

@@ -77,7 +77,6 @@ Instructions
 .. _mamba create: https://mamba.readthedocs.io/en/latest/user_guide/mamba.html#quickstart
 .. _mamba install: https://mamba.readthedocs.io/en/latest/user_guide/mamba.html#quickstart
 
-
 Updating
 --------
 
@@ -95,3 +94,24 @@ To update to a specific version of ``xcdat``:
 
    >>> mamba activate <ENV_NAME>
    >>> mamba update xcdat=<MAJOR.MINOR.PATCH>
+
+Jupyter Users set ``ESMFMKFILE`` env variable
+---------------------------------------------
+
+If you are a Jupyter user, the ``ESMFMKFILE`` environment variable will need to be set
+either directly on the machine or through your Jupyter Notebook.
+
+This env variable is normally set when calling ``conda activate`` with the conda
+environment that has ``xesmf``. However, Jupyter does not run ``conda activate`` when using
+the Python kernel associated with the environment so ``ESMFMKFILE`` is not set, resulting 
+in ``ImportError: The ESMFMKFILE environment variable is not available.`` (related `GitHub
+Issue <https://github.com/xCDAT/xcdat/issues/574>`_).
+
+To set the ``ESMFMKFILE`` in a Jupyter Notebook add:
+
+.. code-block:: python
+
+   >>> import os
+   >>> os.environ['ESMFMKFILE'] = 'conda-envs/xcdat/lib/esmf.mk'
+   >>>
+   >>> import xcdat

docs/getting-started-guide/overview.rst

@@ -132,7 +132,7 @@ Things We Are Striving For
 * Support for parallelism using `dask`_ where it is both possible and makes sense
 
 .. _Metadata Interpretation: https://xcdat.readthedocs.io/en/stable/faqs.html#metadata-interpretation
-.. _xESMF: https://pangeo-xesmf.readthedocs.io/en/latest/
+.. _xESMF: https://xesmf.readthedocs.io/en/latest/
 .. _regrid2: https://cdms.readthedocs.io/en/latest/regrid2.html
 .. _xgcm: https://xgcm.readthedocs.io/en/latest/index.html
 .. _dask: https://dask.org/

xcdat/regridder/accessor.py

@@ -135,7 +135,7 @@ def horizontal(
 
         Supported tools, methods and grids:
 
-        - xESMF (https://pangeo-xesmf.readthedocs.io/en/latest/)
+        - xESMF (https://xesmf.readthedocs.io/en/latest/)
            - Methods: Bilinear, Conservative, Conservative Normed, Patch, Nearest s2d, or Nearest d2s.
            - Grids: Rectilinear, or Curvilinear.
            - Find options at :py:func:`xcdat.regridder.xesmf.XESMFRegridder`