Merge pull request #89 from kthyng/docs

updated docs and associated items

Author: kthyng

docs/conf.py

@@ -18,7 +18,7 @@
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 # see https://pypi.org/project/setuptools-scm/ for details
-from pkg_resources import get_distribution
+from importlib.metadata import version as imversion
 
 
 print("python exec:", sys.executable)
@@ -32,10 +32,10 @@
 # -- Project information -----------------------------------------------------
 
 project = "extract_model"
-copyright = "2022, Kristen Thyng"
+copyright = "2022-2023, Kristen Thyng"
 author = "Kristen Thyng"
 
-release = get_distribution("extract_model").version
+release = imversion("extract_model")
 # for example take major/minor
 version = ".".join(release.split(".")[:2])
 
@@ -85,13 +85,22 @@
 #     "xoak",
 # ]
 
+# https://myst-nb.readthedocs.io/en/v0.9.0/use/execute.html
+jupyter_execute_notebooks = "off"
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ["_build", "**.ipynb_checkpoints", "Thumbs.db", ".DS_Store"]
+exclude_patterns = [
+    "_build",
+    "**.ipynb_checkpoints",
+    "Thumbs.db",
+    ".DS_Store",
+    "_old_docs",
+]
 
 
 # -- Options for HTML output -------------------------------------------------
@@ -109,6 +118,11 @@
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ["_static"]
 
+# https://myst-nb.readthedocs.io/en/v0.13.0/use/execute.html#execution-timeout
+# had this message:
+# WARNING: 'execution_timeout' is deprecated for 'nb_execution_timeout' [mystnb.config]
+# WARNING: 'execution_allow_errors' is deprecated for 'nb_execution_allow_errors' [mystnb.config]
+nb_execution_timeout = 180  # seconds.
 
 # -- nbsphinx specific options ----------------------------------------------
 # this allows notebooks to be run even if they produce errors.

docs/environment.yml

@@ -8,8 +8,7 @@ dependencies:
    - cf_xarray
    - cmocean
    - dask <=2022.05.0 # for xESMF, https://github.com/axiom-data-science/extract_model/issues/49
-   - extract_model
-   - matplotlib
+   - matplotlib-base
    - netcdf4
    - numpy <1.24  # https://github.com/numba/numba/issues/8615#issuecomment-1360792615
    - numba  # required by xesmf

docs/index.rst

@@ -3,27 +3,30 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-`extract_model`
-===============
+Welcome to extract_model's documentation!
+=========================================
 
 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.
 
+Installation
+------------
+
 To install from conda-forge:
 
-  >>> conda install -c conda-forge ocean-model-skill-assessor
+  >>> conda install -c conda-forge extract_model
 
 To install from PyPI:
 
-  >>> pip install cf-pandas
+  >>> pip install extract_model
 
 .. toctree::
    :maxdepth: 2
    :hidden:
    :caption: Examples and demos
 
-   models.md
-   unstructured_subsetting.md
-   ts_work.md
+   models.ipynb
+   unstructured_subsetting.ipynb
+   ts_work.ipynb
    api
 
 .. toctree::