Merge pull request #10 from ESMG/dev

Finalize release 0.3.0

Author: jr3cermak

.github/workflows/base.yml

@@ -45,17 +45,21 @@ jobs:
           echo "🔎 The name of your branch is ${{ github.ref }} and your repository is ${{ github.repository }}."
           echo "💡 The ${{ github.repository }} repository has been cloned to the runner."
           echo "🖥️ The workflow is now ready to test your code on the runner."
-          uname -a
-          pwd
-          df -h
-          printenv
+          mkdir -p output
+          uname -a > output/env.txt
+          pwd >> output/env.txt
+          df -h >> output/env.txt
+          df -h . >> output/env.txt
+          printenv >> output/env.txt
 
       # The worker drops you in the middle of your checked out repository
       - name: Install
         run: |
-          conda env create -q -f conda/gridTools_export.yml
+          conda env create -q -f conda/gridTools_export-linux-64.yml
           conda activate gridTools
+          conda list > output/conda.txt
           python -m pip install -q -e .
+          pip list > output/pip.txt
 
       # Run tests
       - name: Tests
@@ -64,5 +68,9 @@ jobs:
           conda activate gridTools
           cd tests
           pytest -rA
-
-
+      # Archive output to github artifacts
+      - name: Archive
+        uses: actions/upload-artifact@v2
+        with:
+          name: artifact-output
+          path: output/*.txt

.readthedocs.yaml

@@ -10,4 +10,4 @@ formats:
    - pdf
 
 conda:
-  environment: binder/environment.yml
+  environment: conda/gridTools_export-linux-64-RTD.yml

README.md

@@ -108,6 +108,11 @@ provided.  Once software and libraries are installed, the remaining
 software should be installable via pip and/or python's virtual
 environment (venv).
 
+**WARNING**: If a new enviroment is to be prepared with `conda/gridTools.yml`,
+be prepared to wait a VERY LONG TIME for conda to resolve the
+environment.  It is highly recommened to load a new environment with
+`conda/gridTools_export.yml` or `conda/gridTools_explicit-linux-64.txt`.
+
 ## Step 2
 
 [Download](https://github.com/ESMG/gridtools/archive/refs/heads/main.zip)
@@ -135,6 +140,15 @@ plan to install a copy of the grid generation software.
 NOTE: These workarounds should be automatically installed with
 an installation of gridtools in step 2 using pip.
 
+## nodejs
+
+OPTIONAL: This package is optional.  If not using **conda**, this package
+is needed to avoid a warning when starting up jupyter.
+
+```
+Could not determine jupyterlab build status without nodejs.
+```
+
 ## numpypi
 
 Portable intrinsics for numpy ([REPO](https://github.com/adcroft/numpypi)).
@@ -151,20 +165,6 @@ xesmf and then pip replaces it with a fixed copy.
 Users using **venv**, a working compiled copy of ESMF and ESMPy need to
 be installed prior to installing gridutils via pip.
 
-# Code contributions
-
-## Lambert Conformal Conic Grid Generation
-Author: Niki Zadeh [REPO](https://github.com/nikizadehgfdl/grid_generation)
- * [regional_grid_spheical.ipynb](https://github.com/nikizadehgfdl/grid_generation/blob/dev/jupynotebooks/regional_grid_spherical.ipynb)
-
-## Portable intrinsics for numpy
-Author: Alistair Adcroft [REPO](https://github.com/adcroft/numpypi)
- * To obtain bitwise-the-same floating-point values in certain non-time-critical calculations.
-
-## ROMS to MOM6 Grid Converter
-Authors: Mehmet Ilicak; Alistair Adcroft [REPO](https://github.com/ESMG/pyroms)
- * [convert_ROMS_grid_to_MOM6.py](https://raw.githubusercontent.com/ESMG/pyroms/python3/examples/grid_MOM6/convert_ROMS_grid_to_MOM6.py)
-
 # More
 
 Until we can activate Sphinx to create our body of documentation we will have to resort
@@ -174,17 +174,17 @@ Documentation:
   * [conda](docs/conda/README.md)
   * [development](docs/development)
     * [CHANGELOG](docs/development/CHANGELOG.md): Development log of changes
-    * [CREDITS](docs/development/CREDITS.md)
+    * [CREDITS](docs/development/CREDITS.md) and citations
     * [Documentation](docs/development/Documentation.md)
     * [DEPLOY](docs/development/DEPLOY.md)
     * [Design](docs/development/Design.md): Design elements for the grid generation library
     * [Important References](docs/development/ImportantReferences.md): Things that helped this project work
     * [Jupyter](docs/development/Jupyter.md): Notes on embeddeding applications within a notebook
     * [python](docs/development/python)
-      * [leaflet](docs/development/python/leaflet.md)
-      * [panel](docs/development/python/panel.md)
-      * [pyroms](docs/development/python/pyroms.md)
-      * [xesmf](docs/development/python/xesmf.md)
+      * [leaflet](docs/development/python/libraries/leaflet.md)
+      * [panel](docs/development/python/libraries/panel.md)
+      * [pyroms](docs/development/python/libraries/pyroms.md)
+      * [xesmf](docs/development/python/libraries/xesmf.md)
     * [TODO](docs/development/TODO.md): Milestones, tasks, todos and wish list items
       * [archive](docs/archive) -- Archive of completed TODOs
       * [releases](docs/releases) -- Release information

binder/environment.yml

@@ -8,7 +8,8 @@ dependencies:
   - _openmp_mutex=4.5=1_gnu
   - alabaster=0.7.12=py_0
   - alsa-lib=1.2.3=h516909a_0
-  - anyio=3.2.0=py37h89c1867_0
+  - anyio=3.2.1=py37h89c1867_0
+  - appdirs=1.4.4=pyh9f0ad1d_0
   - argon2-cffi=20.1.0=py37h5e8e339_2
   - async_generator=1.10=py_0
   - attrs=21.2.0=pyhd8ed1ab_0
@@ -18,17 +19,22 @@ dependencies:
   - backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0
   - bleach=3.3.0=pyh44b312d_0
   - bokeh=2.3.2=py37h89c1867_0
+  - boost-cpp=1.74.0=hc6e9bd1_3
   - brotlipy=0.7.0=py37h5e8e339_1001
   - bzip2=1.0.8=h7f98852_4
   - c-ares=1.17.1=h7f98852_1
   - ca-certificates=2021.5.30=ha878542_0
+  - cairo=1.16.0=h6cf1ce9_1008
   - cartopy=0.19.0.post1=py37h0c48da3_0
   - certifi=2021.5.30=py37h89c1867_0
   - cf_xarray=0.5.2=pyh6c4a22f_0
   - cffi=1.14.5=py37hc58025e_0
+  - cfitsio=3.470=hb418390_7
   - cftime=1.5.0=py37h6f94858_0
   - chardet=4.0.0=py37h89c1867_1
-  - click=8.0.1=py37h89c1867_0
+  - click=7.1.2=pyh9f0ad1d_0
+  - click-plugins=1.1.1=py_0
+  - cligj=0.7.2=pyhd8ed1ab_0
   - cloudpickle=1.6.0=py_0
   - colorama=0.4.4=pyh9f0ad1d_0
   - colorcet=2.0.6=py_0
@@ -40,34 +46,44 @@ dependencies:
   - cycler=0.10.0=py_2
   - cython=0.29.23=py37hcd2ae1e_1
   - cytoolz=0.11.0=py37h5e8e339_3
-  - dask=2021.6.1=pyhd8ed1ab_0
-  - dask-core=2021.6.1=pyhd8ed1ab_0
+  - dask=2021.6.2=pyhd8ed1ab_0
+  - dask-core=2021.6.2=pyhd8ed1ab_0
   - dataclasses=0.8=pyhc8e2a94_1
   - datashader=0.13.0=py_0
   - datashape=0.5.4=py_1
   - dbus=1.13.6=h48d8840_2
   - decorator=5.0.9=pyhd8ed1ab_0
   - defusedxml=0.7.1=pyhd8ed1ab_0
-  - distributed=2021.6.1=py37h89c1867_0
+  - distributed=2021.6.2=py37h89c1867_0
   - docrep=0.2.7=py_0
   - docutils=0.16=py37h89c1867_3
   - entrypoints=0.3=pyhd8ed1ab_1003
-  - esmf=8.1.1=nompi_hb4f3075_0
-  - esmpy=8.1.1=nompi_py37hff16fce_0
+  - esmf=8.1.0=nompi_hed08645_0
+  - esmpy=8.1.0=nompi_py37hff16fce_0
   - expat=2.4.1=h9c3ff4c_0
+  - fiona=1.8.18=py37h17d6ad9_1
   - fontconfig=2.13.1=hba837de_1005
   - freetype=2.10.4=h0708190_1
-  - fsspec=2021.6.0=pyhd8ed1ab_0
+  - freexl=1.0.6=h7f98852_0
+  - fsspec=2021.6.1=pyhd8ed1ab_0
   - future=0.18.2=py37h89c1867_3
+  - gdal=3.2.1=py37hc5bc4e4_7
+  - geopandas=0.9.0=pyhd8ed1ab_0
   - geos=3.9.1=h9c3ff4c_2
+  - geotiff=1.6.0=h2b14fbe_4
+  - geoviews=1.9.1=py_0
+  - geoviews-core=1.9.1=py_0
   - gettext=0.19.8.1=h0b5b191_1005
+  - giflib=5.2.1=h36c2ea0_2
   - glib=2.68.3=h9c3ff4c_0
   - glib-tools=2.68.3=h9c3ff4c_0
   - gst-plugins-base=1.18.4=hf529b03_2
   - gstreamer=1.18.4=h76c114f_2
   - hdf4=4.2.15=h10796ff_3
   - hdf5=1.10.6=nompi_h6a2412b_1114
   - heapdict=1.0.1=py_0
+  - holoviews=1.14.4=py_0
+  - hvplot=0.7.2=py_0
   - icu=68.1=h58526e2_0
   - idna=2.10=pyh9f0ad1d_0
   - imagesize=1.2.0=py_0
@@ -77,64 +93,73 @@ dependencies:
   - ipykernel=5.5.5=py37h085eea5_0
   - ipython=7.24.1=py37h085eea5_0
   - ipython_genutils=0.2.0=py_1
-  - jbig=2.1=h7f98852_2003
+  - ipywidgets=7.6.3=pyhd3deb0d_0
   - jedi=0.18.0=py37h89c1867_2
   - jinja2=3.0.1=pyhd8ed1ab_0
   - jpeg=9d=h36c2ea0_0
+  - json-c=0.15=h98cffda_0
   - json5=0.9.5=pyh9f0ad1d_0
   - jsonschema=3.2.0=pyhd8ed1ab_3
+  - jupyter=1.0.0=py37h89c1867_6
   - jupyter_client=6.1.12=pyhd8ed1ab_0
+  - jupyter_console=6.4.0=pyhd8ed1ab_0
   - jupyter_core=4.7.1=py37h89c1867_0
-  - jupyter_server=1.8.0=pyhd8ed1ab_0
+  - jupyter_server=1.9.0=pyhd8ed1ab_0
   - jupyterlab=3.0.16=pyhd8ed1ab_0
   - jupyterlab_pygments=0.1.2=pyh9f0ad1d_0
   - jupyterlab_server=2.6.0=pyhd8ed1ab_0
+  - jupyterlab_widgets=1.0.0=pyhd8ed1ab_1
+  - kealib=1.4.14=hcc255d8_2
   - kiwisolver=1.3.1=py37h2527ec5_1
   - krb5=1.19.1=hcc1bbae_0
   - latexcodec=2.0.1=pyh9f0ad1d_0
   - lcms2=2.12=hddcbb42_0
   - ld_impl_linux-64=2.35.1=hea4e1c9_2
-  - lerc=2.2.1=h9c3ff4c_0
   - libblas=3.9.0=9_openblas
   - libcblas=3.9.0=9_openblas
   - libclang=11.1.0=default_ha53f305_1
   - libcurl=7.77.0=h2574ce0_0
-  - libdeflate=1.7=h7f98852_5
+  - libdap4=3.20.6=hd7c4107_2
   - libedit=3.1.20191231=he28a2e2_2
   - libev=4.33=h516909a_1
   - libevent=2.1.10=hcdb4288_3
   - libffi=3.3=h58526e2_2
   - libgcc-ng=9.3.0=h2828fa1_19
+  - libgdal=3.2.1=h38ff51b_7
   - libgfortran-ng=9.3.0=hff62375_19
   - libgfortran5=9.3.0=hff62375_19
   - libglib=2.68.3=h3e27bee_0
   - libgomp=9.3.0=h2828fa1_19
   - libiconv=1.16=h516909a_0
+  - libkml=1.3.0=h238a007_1013
   - liblapack=3.9.0=9_openblas
   - libllvm10=10.0.1=he513fc3_3
   - libllvm11=11.1.0=hf817b99_2
-  - libnetcdf=4.8.0=nompi_hcd642e3_103
+  - libnetcdf=4.7.4=nompi_h56d31a8_107
   - libnghttp2=1.43.0=h812cca2_0
   - libogg=1.3.4=h7f98852_1
   - libopenblas=0.3.15=pthreads_h8fe5266_1
   - libopus=1.3.1=h7f98852_1
   - libpng=1.6.37=h21135ba_2
   - libpq=13.3=hd57d9b9_0
+  - librttopo=1.1.0=h1185371_6
   - libsodium=1.0.18=h36c2ea0_1
+  - libspatialindex=1.9.3=h9c3ff4c_3
+  - libspatialite=5.0.1=he52d314_3
   - libssh2=1.9.0=ha56f1ee_6
   - libstdcxx-ng=9.3.0=h6de172a_19
-  - libtiff=4.3.0=hf544144_1
+  - libtiff=4.2.0=hbd63e13_2
   - libuuid=2.32.1=h7f98852_1000
+  - libuv=1.41.0=h7f98852_0
   - libvorbis=1.3.7=h9c3ff4c_0
   - libwebp-base=1.2.0=h7f98852_2
   - libxcb=1.13=h7f98852_1003
   - libxkbcommon=1.0.3=he3ba5ed_0
   - libxml2=2.9.12=h72842e0_0
-  - libzip=1.8.0=h4de3113_0
   - llvmlite=0.36.0=py37h9d7f4d0_0
   - locket=0.2.0=py_2
   - lz4-c=1.9.3=h9c3ff4c_0
-  - m2r2=0.2.7=pyhd3deb0d_0
+  - m2r2=0.2.8=pyhd8ed1ab_0
   - markdown=3.3.4=pyhd8ed1ab_0
   - markupsafe=2.0.1=py37h5e8e339_0
   - matplotlib=3.4.2=py37h89c1867_0
@@ -144,27 +169,30 @@ dependencies:
   - more-itertools=8.8.0=pyhd8ed1ab_0
   - msgpack-python=1.0.2=py37h2527ec5_1
   - multipledispatch=0.6.0=py_0
-  - mysql-common=8.0.25=ha770c72_2
-  - mysql-libs=8.0.25=hfa10184_2
+  - munch=2.5.0=py_0
+  - mysql-common=8.0.25=ha770c72_0
+  - mysql-libs=8.0.25=h935591d_0
   - nbclassic=0.3.1=pyhd8ed1ab_1
   - nbclient=0.5.3=pyhd8ed1ab_0
-  - nbconvert=6.0.7=py37h89c1867_3
+  - nbconvert=6.1.0=py37h89c1867_0
   - nbformat=5.1.3=pyhd8ed1ab_0
   - ncurses=6.2=h58526e2_4
   - nest-asyncio=1.5.1=pyhd8ed1ab_0
-  - netcdf-fortran=4.5.3=nompi_hf3f1587_104
-  - netcdf4=1.5.7=nompi_py37h946d57d_100
+  - netcdf-fortran=4.5.3=nompi_h996563d_103
+  - netcdf4=1.5.6=nompi_py37hf7b6e46_102
+  - nodejs=15.14.0=h92b4a50_0
   - notebook=6.4.0=pyha770c72_0
   - nspr=4.30=h9c3ff4c_0
   - nss=3.67=hb5efdd6_0
   - numba=0.53.1=py37hb11d6e1_1
-  - numpy=1.20.3=py37h038b26d_1
+  - numpy=1.21.0=py37h038b26d_0
   - olefile=0.46=pyh9f0ad1d_1
   - openjpeg=2.4.0=hb52868f_1
   - openssl=1.1.1k=h7f98852_0
+  - owslib=0.24.1=pyhd8ed1ab_0
   - packaging=20.9=pyh44b312d_0
-  - pandas=1.2.4=py37h219a48f_0
-  - pandoc=2.14.0.2=h7f98852_0
+  - pandas=1.2.5=py37h219a48f_0
+  - pandoc=2.14.0.3=h7f98852_0
   - pandocfilters=1.4.2=py_1
   - panel=0.11.3=py_0
   - param=1.10.1=py_0
@@ -175,10 +203,16 @@ dependencies:
   - pickleshare=0.7.5=py_1003
   - pillow=8.2.0=py37h4600e1f_1
   - pip=21.1.2=pyhd8ed1ab_0
+  - pixman=0.40.0=h36c2ea0_0
   - pluggy=0.13.1=py37h89c1867_4
+  - pooch=1.4.0=pyhd8ed1ab_0
+  - poppler=0.89.0=h2de54a5_5
+  - poppler-data=0.4.10=0
+  - postgresql=13.3=h2510834_0
   - proj=7.2.0=h277dcde_2
   - prometheus_client=0.11.0=pyhd8ed1ab_0
   - prompt-toolkit=3.0.19=pyha770c72_0
+  - prompt_toolkit=3.0.19=hd8ed1ab_0
   - psutil=5.8.0=py37h5e8e339_1
   - pthread-stubs=0.4=h36c2ea0_1001
   - ptyprocess=0.7.0=pyhd3deb0d_0
@@ -211,11 +245,15 @@ dependencies:
   - pyyaml=5.4.1=py37h5e8e339_0
   - pyzmq=22.1.0=py37h336d617_0
   - qt=5.12.9=hda022c4_4
+  - qtconsole=5.1.0=pyhd8ed1ab_0
+  - qtpy=1.9.0=py_0
   - readline=8.1=h46c0cb4_0
   - requests=2.25.1=pyhd3deb0d_0
+  - requests-unixsocket=0.2.0=py_0
+  - rtree=0.9.7=py37h0b55af0_1
   - ruamel_yaml=0.15.80=py37h5e8e339_1004
   - scipy=1.6.3=py37h29e03ee_0
-  - send2trash=1.5.0=py_0
+  - send2trash=1.7.1=pyhd8ed1ab_0
   - setuptools=49.6.0=py37h89c1867_3
   - shapely=1.7.1=py37h2d1e849_5
   - six=1.16.0=pyh6c4a22f_0
@@ -235,27 +273,41 @@ dependencies:
   - tblib=1.7.0=pyhd8ed1ab_0
   - terminado=0.10.1=py37h89c1867_0
   - testpath=0.5.0=pyhd8ed1ab_0
+  - tiledb=2.2.9=h91fcb0e_0
   - tk=8.6.10=h21135ba_1
   - toml=0.10.2=pyhd8ed1ab_0
   - toolz=0.11.1=py_0
   - tornado=6.1=py37h5e8e339_1
   - tqdm=4.61.1=pyhd8ed1ab_0
   - traitlets=5.0.5=py_0
   - typing_extensions=3.10.0.0=pyha770c72_0
+  - tzcode=2021a=h7f98852_1
+  - tzdata=2021a=he74cb21_0
   - urllib3=1.26.5=pyhd8ed1ab_0
   - wcwidth=0.2.5=pyh9f0ad1d_2
   - webencodings=0.5.1=py_1
   - websocket-client=0.57.0=py37h89c1867_4
   - wheel=0.36.2=pyhd3deb0d_0
+  - widgetsnbextension=3.5.1=py37h89c1867_4
   - xarray=0.18.2=pyhd8ed1ab_0
+  - xerces-c=3.2.3=h9d8b166_2
   - xesmf=0.5.3=pyhd8ed1ab_0
   - xgcm=0.5.2=pyhd8ed1ab_0
+  - xorg-kbproto=1.0.7=h7f98852_1002
+  - xorg-libice=1.0.10=h7f98852_0
+  - xorg-libsm=1.2.3=hd9c2040_1000
+  - xorg-libx11=1.7.2=h7f98852_0
   - xorg-libxau=1.0.9=h7f98852_0
   - xorg-libxdmcp=1.1.3=h7f98852_0
+  - xorg-libxext=1.3.4=h7f98852_1
+  - xorg-libxrender=0.9.10=h7f98852_1003
+  - xorg-renderproto=0.11.1=h7f98852_1002
+  - xorg-xextproto=7.3.0=h7f98852_1002
+  - xorg-xproto=7.0.31=h7f98852_1007
   - xz=5.2.5=h516909a_1
   - yaml=0.2.5=h516909a_0
   - zeromq=4.3.4=h9c3ff4c_0
   - zict=2.0.0=py_0
   - zipp=3.4.1=pyhd8ed1ab_0
   - zlib=1.2.11=h516909a_1010
-  - zstd=1.5.0=ha95c52a_0
+  - zstd=1.4.9=ha95c52a_0