Merge pull request #5 from kthyng/main

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axiom-data-science · May 17, 2021 · 70fa27c · 70fa27c
2 parents 354c1e5 + d71ed77
commit 70fa27c
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diff --git a/docs/api.rst b/docs/api.rst
diff --git a/docs/environment.yml b/docs/environment.yml
@@ -4,6 +4,12 @@ dependencies:
    # If your docs code examples depend on other packages add them here
    - numpy
    - xarray
+   - cf-xarray
+   - matplotlib
+   - cmocean
+   # use mac dependencies
+   - esmf=8.1.1=mpi_openmpi_h047fafc_0
+   - esmpy=8.1.1=mpi_openmpi_py38hf504846_0
    # These are needed for the docs themselves
    - numpydoc
    - sphinx
@@ -13,11 +19,15 @@ dependencies:
    - nbformat
    - ipykernel
    - pandoc
+   - recommonmark
    - pip
    - pip:
+     - git+https://github.com/axiom-data-science/extract_model.git#egg=extract_model
+     - git+https://github.com/pangeo-data/xESMF.git#egg=xESMF
+     - xcmocean
      - docrep<=0.2.7
      - nbsphinx
      - jupyter_client
      - sphinx_pangeo_theme
      - sphinx-copybutton
-     - sphinxcontrib-srclinks
+     - sphinxcontrib-srclinks
diff --git a/docs/index.rst b/docs/index.rst
@@ -3,22 +3,15 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to extract_model's documentation!
-=======================================
+`extract_model`
+===============
 
-This is an awesome description of extract_model, written in `reStructuredText`_.
-
-You can contribute new sections by either adding a new file (see ``new_section.rst``) or just putting a jupyter notebook
-in the ``docs`` folder (see ``new_section_notebook.ipynb``).
-
-In either case, make sure to add an entry in the ``.. toctree::``. Check out ``index.rst`` how it was done for the above examples.
+Use `extract_model` to read select output from model output files by time and/or space. Output will be selected using `xarray` by a combination of interpolation and index selection. Horizontal interpolation is accomplished using `xESMF` and time interpolation is done with `xarray`'s native 1D interpolation. Currently vertical interpolation is only possible using `xarray`'s 1D interpolation too and is not set up to interpolate in 4D as would be required for ROMS output if not simply selecting the surface layer.
 
 .. toctree::
    :maxdepth: 2
 
-   new_section
-   new_section_notebook
-   api
+   models
 
 
 
@@ -28,5 +21,3 @@ Indices and tables
 * :ref:`genindex`
 * :ref:`modindex`
 * :ref:`search`
-
-.. _reStructuredText: https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html
diff --git a/docs/models.ipynb b/docs/models.ipynb
@@ -10,8 +10,6 @@
     "import cf_xarray\n",
     "import numpy as np\n",
     "import xarray as xr\n",
-    "import xgcm\n",
-    "import xesmf as xe\n",
     "import matplotlib.pyplot as plt\n",
     "import xcmocean\n",
     "import cmocean.cm as cmo\n",
@@ -26,20 +24,12 @@
     "# Generically access model output"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "id": "231623aa-e963-4f16-86b7-0ffdfa104f0e",
-   "metadata": {},
-   "source": [
-    "## Test"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "1ed06a35-45ab-4ee7-8039-ff11f164caed",
    "metadata": {},
    "source": [
-    "### MOM6"
+    "## MOM6"
    ]
   },
   {
@@ -70,15 +60,15 @@
    "id": "579965a6-086c-4a52-8e40-a1ed321b2198",
    "metadata": {},
    "source": [
-    "#### grid point"
+    "### grid point"
    ]
   },
   {
    "cell_type": "markdown",
    "id": "3a1eea02-288d-40b4-bed5-9b60051f27ed",
    "metadata": {},
    "source": [
-    "##### horizontal interp, vertical and time isel"
+    "#### horizontal interp, vertical and time isel"
    ]
   },
   {
@@ -129,7 +119,7 @@
    "id": "e833f054-c0ac-4866-81b8-36ac2db7d822",
    "metadata": {},
    "source": [
-    "##### horizontal and vertical interp, time isel"
+    "#### horizontal and vertical interp, time isel"
    ]
   },
   {
@@ -178,15 +168,15 @@
    "id": "a139e03b-3219-4283-9863-745b59890ff1",
    "metadata": {},
    "source": [
-    "#### not grid point"
+    "### not grid point"
    ]
   },
   {
    "cell_type": "markdown",
    "id": "292eab46-3d23-4c85-8d45-f8cd22c72675",
    "metadata": {},
    "source": [
-    "##### inside domain"
+    "#### inside domain"
    ]
   },
   {
@@ -260,7 +250,7 @@
    "id": "513df367-84bd-450b-b7d3-fa258b2bc75f",
    "metadata": {},
    "source": [
-    "##### outside domain"
+    "#### outside domain"
    ]
   },
   {
@@ -380,7 +370,7 @@
    "id": "4531d5bd-7746-4ade-843e-bc0be3a52433",
    "metadata": {},
    "source": [
-    "#### points (locstream)\n",
+    "### points (locstream)\n",
     "\n",
     "Unstructured pairs of lon/lat locations instead of grids of lon/lat locations, using `locstream`."
    ]
@@ -438,7 +428,7 @@
    "id": "e0940537-0911-4f77-92d5-5bf3b81ea055",
    "metadata": {},
    "source": [
-    "#### grid of known locations"
+    "### grid of known locations"
    ]
   },
   {
@@ -487,7 +477,7 @@
    "id": "9158bffd-4a87-4db4-927e-0a5d8dc7370c",
    "metadata": {},
    "source": [
-    "#### grid of new locations"
+    "### grid of new locations"
    ]
   },
   {
@@ -561,7 +551,7 @@
    "id": "01ed35fe-cd31-44b0-90d2-423dc14f3393",
    "metadata": {},
    "source": [
-    "### HYCOM"
+    "## HYCOM"
    ]
   },
   {
@@ -589,7 +579,7 @@
    "id": "c79341d1-492e-4896-8c49-aa8db06a7aba",
    "metadata": {},
    "source": [
-    "#### grid point"
+    "### grid point"
    ]
   },
   {
@@ -629,15 +619,15 @@
    "id": "40f3ca75-f2af-43bf-9f8c-0818b7072d2a",
    "metadata": {},
    "source": [
-    "#### not grid point"
+    "### not grid point"
    ]
   },
   {
    "cell_type": "markdown",
    "id": "caf72205-aec3-42dc-b77f-b12a931be41c",
    "metadata": {},
    "source": [
-    "##### inside domain"
+    "#### inside domain"
    ]
   },
   {
@@ -678,7 +668,7 @@
    "id": "c2abd653-de42-44f9-8350-6827657dae47",
    "metadata": {},
    "source": [
-    "##### outside domain"
+    "#### outside domain"
    ]
   },
   {
@@ -819,7 +809,7 @@
    "id": "86bce0f5-0be3-4f9d-a097-c7f39e7f8788",
    "metadata": {},
    "source": [
-    "#### points (locstream)\n",
+    "### points (locstream)\n",
     "\n",
     "Unstructured pairs of lon/lat locations instead of grids of lon/lat locations, using `locstream`."
    ]
@@ -878,7 +868,7 @@
    "id": "5aee17b6-55f7-43bf-b1ce-0040fe6506a0",
    "metadata": {},
    "source": [
-    "#### grid of known locations"
+    "### grid of known locations"
    ]
   },
   {
@@ -931,7 +921,7 @@
    "id": "dc123ada-7da4-4a43-8da0-5b905dd61e19",
    "metadata": {},
    "source": [
-    "#### grid of new locations"
+    "### grid of new locations"
    ]
   },
   {
@@ -1015,7 +1005,7 @@
    "id": "d12ac238-33ac-42ed-bcdc-9c7e18322e69",
    "metadata": {},
    "source": [
-    "### ROMS"
+    "## ROMS"
    ]
   },
   {
@@ -1782,7 +1772,7 @@
    "id": "99752714-ac31-423f-812c-fd403cfd944f",
    "metadata": {},
    "source": [
-    "#### grid point"
+    "### grid point"
    ]
   },
   {
@@ -1833,15 +1823,15 @@
    "id": "e52cbf63-f0cb-4674-b799-f9922cf2ede3",
    "metadata": {},
    "source": [
-    "#### not grid point"
+    "### not grid point"
    ]
   },
   {
    "cell_type": "markdown",
    "id": "9c872e5d-8096-4967-83ec-d39740cedda5",
    "metadata": {},
    "source": [
-    "##### inside domain"
+    "#### inside domain"
    ]
   },
   {
@@ -1914,7 +1904,7 @@
    "id": "0157430c-f673-4166-b982-87ef9e886fa3",
    "metadata": {},
    "source": [
-    "##### outside domain"
+    "#### outside domain"
    ]
   },
   {
@@ -2044,7 +2034,7 @@
    "id": "0b61c634-853c-4d74-9ae8-52525c978d3a",
    "metadata": {},
    "source": [
-    "#### points (locstream)\n",
+    "### points (locstream)\n",
     "\n",
     "Unstructured pairs of lon/lat locations instead of grids of lon/lat locations, using `locstream`."
    ]
@@ -2106,7 +2096,7 @@
    "id": "2a12dafa-7997-4a16-9bab-4afab1c4d869",
    "metadata": {},
    "source": [
-    "#### grid of known locations"
+    "### grid of known locations"
    ]
   },
   {
@@ -2155,7 +2145,7 @@
    "id": "c1ad2d87-2f7a-4b7b-8654-207803f5e935",
    "metadata": {},
    "source": [
-    "#### grid of new locations"
+    "### grid of new locations"
    ]
   },
   {
@@ -2241,7 +2231,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.8"
+   "version": "3.8.10"
   }
  },
  "nbformat": 4,

diff --git a/docs/new_section.rst b/docs/new_section.rst