Merge pull request #88 from kthyng/old_xoak

Old xoak

.pre-commit-config.yaml

@@ -42,9 +42,10 @@ repos:
     language_version: python3
 
 # - repo: https://github.com/pre-commit/mirrors-mypy
-#   rev: v0.770
+#   rev: v0.982
 #   hooks:
 #   - id: mypy
+#     additional_dependencies: [types-setuptools, types-PyYAML]
 #     exclude: docs/source/conf.py
 #     args: [--ignore-missing-imports]
 

.readthedocs.yaml

@@ -5,6 +5,11 @@ build:
   tools:
     python: "mambaforge-4.10"
 
+python:
+  install:
+    - method: pip
+      path: ./
+
 conda:
     environment: docs/environment.yml
 

ci/environment-py3.10-win.yml

@@ -6,16 +6,16 @@ dependencies:
   - cf_xarray>=0.6
   - dask
   - netcdf4
-  - numpy
+  - numpy <1.24  # https://github.com/numba/numba/issues/8615#issuecomment-1360792615
   - pip
   - requests
   - scikit-learn  # used by xoak for tree
   - xarray
-  # - xoak
+  - xoak
   - pytest
   - pytest-benchmark
   - pip:
     - codecov
     - pytest-cov
     - coverage[toml]
-    - git+https://github.com/kthyng/xoak@include_distances
+    # - git+https://github.com/kthyng/xoak@include_distances

ci/environment-py3.10.yml

@@ -6,17 +6,17 @@ dependencies:
   - cf_xarray>=0.6
   - dask <=2022.05.0 # for xESMF, https://github.com/axiom-data-science/extract_model/issues/49
   - netcdf4
-  - numpy
+  - numpy <1.24  # https://github.com/numba/numba/issues/8615#issuecomment-1360792615
   - pip
   - requests
   - scikit-learn  # used by xoak for tree
   - xarray
   - xesmf
-  # - xoak
+  - xoak
   - pytest
   - pytest-benchmark
   - pip:
     - codecov
     - pytest-cov
     - coverage[toml]
-    - git+https://github.com/kthyng/xoak@include_distances
+    # - git+https://github.com/kthyng/xoak@include_distances

ci/environment-py3.8-win.yml

@@ -6,16 +6,16 @@ dependencies:
   - cf_xarray>=0.6
   - dask
   - netcdf4
-  - numpy
+  - numpy <1.24  # https://github.com/numba/numba/issues/8615#issuecomment-1360792615
   - pip
   - requests
   - scikit-learn  # used by xoak for tree
   - xarray
-  # - xoak
+  - xoak
   - pytest
   - pytest-benchmark
   - pip:
     - codecov
     - pytest-cov
     - coverage[toml]
-    - git+https://github.com/kthyng/xoak@include_distances
+    # - git+https://github.com/kthyng/xoak@include_distances

ci/environment-py3.8.yml

@@ -6,17 +6,17 @@ dependencies:
   - cf_xarray>=0.6
   - dask <=2022.05.0 # for xESMF, https://github.com/axiom-data-science/extract_model/issues/49
   - netcdf4
-  - numpy
+  - numpy <1.24  # https://github.com/numba/numba/issues/8615#issuecomment-1360792615
   - pip
   - requests
   - scikit-learn  # used by xoak for tree
   - xarray
   - xesmf
-  # - xoak
+  - xoak
   - pytest
   - pytest-benchmark
   - pip:
     - codecov
     - pytest-cov
     - coverage[toml]
-    - git+https://github.com/kthyng/xoak@include_distances
+    # - git+https://github.com/kthyng/xoak@include_distances

ci/environment-py3.9-win.yml

@@ -6,16 +6,16 @@ dependencies:
   - cf_xarray>=0.6
   - dask
   - netcdf4
-  - numpy
+  - numpy <1.24  # https://github.com/numba/numba/issues/8615#issuecomment-1360792615
   - pip
   - requests
   - scikit-learn  # used by xoak for tree
   - xarray
-  # - xoak
+  - xoak
   - pytest
   - pytest-benchmark
   - pip:
     - codecov
     - pytest-cov
     - coverage[toml]
-    - git+https://github.com/kthyng/xoak@include_distances
+    # - git+https://github.com/kthyng/xoak@include_distances

ci/environment-py3.9.yml

@@ -6,17 +6,17 @@ dependencies:
   - cf_xarray>=0.6
   - dask <=2022.05.0 # for xESMF, https://github.com/axiom-data-science/extract_model/issues/49
   - netcdf4
-  - numpy
+  - numpy <1.24  # https://github.com/numba/numba/issues/8615#issuecomment-1360792615
   - pip
   - requests
   - scikit-learn  # used by xoak for tree
   - xarray
   - xesmf
-  # - xoak
+  - xoak
   - pytest
   - pytest-benchmark
   - pip:
     - codecov
     - pytest-cov
     - coverage[toml]
-    - git+https://github.com/kthyng/xoak@include_distances
+    # - git+https://github.com/kthyng/xoak@include_distances

docs/api.rst

@@ -1,12 +1,17 @@
-:mod:`API`
-----------------------------
+API
+===
 
-`extract_model` Python API
-==========================
+.. currentmodule:: extract_model
 
 
-.. automodule:: extract_model.extract_model
-   :members:
-   :inherited-members:
-   :undoc-members:
-   :show-inheritance:
+.. autosummary::
+   :toctree: generated/
+   :recursive:
+
+   extract_model
+   utils
+   accessor
+   sorting
+   model_type
+   grids.triangular_mesh
+   xr.triangular_mesh_netcdf

docs/conf.py

@@ -48,19 +48,25 @@
     "sphinx.ext.autodoc",
     "sphinx.ext.viewcode",
     "sphinx.ext.napoleon",
-    "nbsphinx",
+    # "nbsphinx",
     "recommonmark",
     "sphinx.ext.mathjax",
     "sphinx.ext.autosummary",
     "sphinx.ext.extlinks",
     "sphinx.ext.intersphinx",
     "numpydoc",
-    "nbsphinx",
+    # "nbsphinx",
     "IPython.sphinxext.ipython_directive",
     "IPython.sphinxext.ipython_console_highlighting",
     "sphinxcontrib.srclinks",
+    "myst_nb",
 ]
 
+# for compiling notebooks with mystnb
+# https://docs.readthedocs.io/en/stable/guides/jupyter.html#using-notebooks-in-other-formats
+nb_custom_formats = {
+    ".md": ["jupytext.reads", {"fmt": "mystnb"}],
+}
 # packages that I don't want to install for docs but package depends on
 # autodoc_mock_imports = [
 #     "cf_xarray",
@@ -93,7 +99,10 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = "pangeo"
+# html_theme = "pangeo"
+html_theme = "furo"
+
+html_title = "extract_model documentation"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,

docs/environment.yml

@@ -5,13 +5,31 @@ channels:
 dependencies:
    - python=3.8
    # If your docs code examples depend on other packages add them here
+   - cf_xarray
+   - cmocean
+   - dask <=2022.05.0 # for xESMF, https://github.com/axiom-data-science/extract_model/issues/49
    - extract_model
+   - matplotlib
+   - netcdf4
+   - numpy <1.24  # https://github.com/numba/numba/issues/8615#issuecomment-1360792615
+   - numba  # required by xesmf
+   - pip
+   - pooch
+   - requests
+   - scikit-learn  # used by xoak for tree
+   - xarray
+   - xcmocean
+   - xesmf  # don't install if on windows
+   - xoak
    # These are needed for the docs themselves
+   - furo
+   - jupytext
    - numpydoc
    - sphinx
    - sphinx_rtd_theme
    - ipython
    - jinja2 #<3.1
+   - myst-nb
    - nbconvert
    - nbformat
    - ipykernel

docs/index.rst

@@ -8,20 +8,36 @@
 
 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.
 
+To install from conda-forge:
+
+  >>> conda install -c conda-forge ocean-model-skill-assessor
+
+To install from PyPI:
+
+  >>> pip install cf-pandas
+
 .. toctree::
    :maxdepth: 2
+   :hidden:
+   :caption: Examples and demos
 
-   models
-   unstructured_subsetting
-   ts_work
-   whats_new
+   models.md
+   unstructured_subsetting.md
+   ts_work.md
    api
 
+.. toctree::
+   :maxdepth: 2
+   :hidden:
+   :caption: Develop docs
+
+   whats_new
+
 
 
-Indices and tables
-==================
+.. Indices and tables
+.. ==================
 
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+.. * :ref:`genindex`
+.. * :ref:`modindex`
+.. * :ref:`search`