Initial commit. Release 0.1.

.gitignore

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-lib/
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README.md

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 # gridtools
-A collection of grid generation tools
+
+A generic set of grid manipulation tools for computer models.  These tools are
+adapted from the ROMS ocean model and for specific use in the MOM6 ocean model.
+One could hope it can be kept generic enough to support any model.  The focus
+is on supporting the MOM6 ocean model.
+
+For in depth details about the MOM6 ocean model, please visit provided
+[wiki](https://github.com/NOAA-GFDL/MOM6-examples/wiki) pages.  Technical
+details about this repository can be found below.  For usage of
+the GridUtils library, please visit the [user manual](docs/manual/GridUtils.md).
+
+Required items:
+ * spherical.py
+ * gridutils.py
+ * app.py
+
+Optional items:
+ * sysinfo.py
+
+Various tools are available to manipulation of new and existing grids in
+an iterative or interactive form.
+
+Python notebooks:
+ * mkGridIterative.ipynb
+ * mkGridInteractive.ipynb
+
+With this software, you should be able to operate in any mode you prefer.
+
+# Operational Modes
+
+## Command Line
+
+Using the command line or writing your own python scripts possible utilizing this library.
+To look at a few examples, please look at the mkGridsExample1.py, mkGridsExample2.py and
+mkGridsExample3.py programs.
+
+## Command Line Widget Mode
+
+ * ipython --pylab
+
+The interpreter, ipython, can run python scripts and notebook scripts.  To run a notebook
+script, you can use `ipython -c "%run your_script.ipynb"`.  Or start ipython, and then
+`%run your_script.ipynb`.
+
+Again, the mkGridsExample.py programs can be run with ipython.
+
+## Jupyter notebook
+
+ * jupyter notebook
+
+These prefer notebook files (ipynb).  Please see the mkGridIterative.ipynb program for a hands
+on way to access the grid generation library.  
+
+A simple graphical user interface (GUI) was built and is available when you run the
+mkGridInteractive.ipynb notebook.
+
+## Jupyter lab
+
+ * jupyter lab
+
+These prefer notebook files (ipynb).  Please see the mkGridIterative.ipynb program for a hands
+on way to access the grid generation library.  
+
+A simple graphical user interface (GUI) was built and is available when you run the
+mkGridInteractive.ipynb notebook.
+
+## mybinder
+
+ * Main: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ESMG/gridtools/main)
+ * Dev: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ESMG/gridtools/dev)
+
+Instead of loading software on your computer, the library and application is hosted on a cloud system.  You do not
+have to install anything on your system to use the cloud system's copy of the grid generation library.
+
+# Application
+
+The grid generation application, mkGridInteractive.ipynb, can be run on a cloud hosting system.  The application has been adapted to work on mybinder.org.
+NOTICE: The mybinder application can take upwards to 30 minutes to build.
+
+Use the following options:
+ * GitHub=https://github.com/ESMG/gridtools
+ * Git ref=main
+ * Launch
+ * Once the server loads, navigate to gridTools/mkMapInteractive.ipynb
+ * Re-run all the cells
+ * Have fun with the grid editor.
+
+# 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)
+
+## Numpy bitwise-the-same floating-point values
+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)
+
+# Installation
+
+If you plan to use the grid generation software on your system, you need to peform the following steps.
+
+## Step 1
+
+[Download](https://github.com/ESMG/gridtools/archive/refs/heads/main.zip) or [clone](https://github.com/ESMG/gridtools.git) the 
+[ESMG/gridtools](https://github.com/ESMG/gridtools) repository.
+
+Discover the full directory path to gridtools/gridTools/lib.   Place the full path in the environment variable `LIBROOT` if you are planning to run
+the python notebooks.  If you are going to use the library in your scripts, simply append the full path to `PYTHONPATH`.  In the future, we will enable
+installation using ptyhon pip.
+
+## Step 2
+
+Install conda or manually install the python libraries and software dependencies that would allow you to run the python scripts or notebooks.
+
+We have pulled together some pre-defined environments.  You may also install an environment yourself.   Please look at the [conda](docs/conda/README.md)
+page for more information about conda.
+
+We currently recommend the *xesmfTools* environment for use with this libaray.
+
+## Step 3
+
+Follow any steps in the "Workarounds" section.
+
+# Workarounds
+
+These are the current workarounds that are required for the grid toolset
+package.  You will need to perform these steps once if you plan to install a
+copy of the grid generation software.
+
+## datashader
+
+The lastest version from github is required for proper operation of bokeh, holoviews and panel which
+are used by the interactive portions of the grid generation library.
+
+[REPO](https://github.com/holoviz/datashader)
+
+Installation:
+  * Download or clone this repository.
+  * Change directory to the datashader directory.
+  * Make sure your conda enviroment is active.
+  * `pip install -e .`
+
+## numpypi
+
+NOTE: This has not been fully implemented yet.  Do not worry about this just yet.
+
+For bitwise-the-same reproducable results, a numpy subset of computational functions are
+provided.  These routines are slower than the numpy native routines.  
+[REPO](https://github.com/adcroft/numpypi)
+
+# More
+
+Until we can activate Sphinx to create our body of documentation we will have to resort
+to upkeep of a manual index.
+
+[Documentation](docs/Documentation.md)
+  * [conda](docs/conda/README.md)
+  * [development](docs/development)
+    * [CHANGELOG](docs/development/CHANGELOG.md): Development log of changes
+    * [CREDITS](docs/development/CREDITS.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)
+    * [TODO](docs/development/TODO.md): Milestones, tasks, todos and wishes
+  * [grids](docs/grids)
+    * [Examples](docs/grids/Examples.md): Descriptions of grids used in examples
+    * [Grids](docs/grids/Grids.md)
+    * [MOM6](docs/grids/MOM6.md): MOM6 grids
+    * [MOM6ROMS](docs/grids/MOM6ROMS.md): Important things between MOM6 and ROMS grids
+    * [ROMS](docs/grids/ROMS.md): ROMS grids
+  * [manual](docs/manual/GridUtils.md): User manual for the GridUtils library
+  * [resources](docs/resources)
+    * [Bathymetry](docs/resources/Bathymetry)
+
+# Development
+
+This project is soliciting help in development.  Please contribute ideas or bug requests using the issues tab.
+Code contributions can be sent via github's pull request process.

conda/base_export.yml

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+name: base
+channels:
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1=main
+  - brotlipy=0.7.0=py38h27cfd23_1003
+  - ca-certificates=2020.10.14=0
+  - certifi=2020.6.20=pyhd3eb1b0_3
+  - cffi=1.14.3=py38h261ae71_2
+  - chardet=3.0.4=py38h06a4308_1003
+  - conda=4.9.2=py38h06a4308_0
+  - conda-package-handling=1.7.2=py38h03888b9_0
+  - cryptography=3.2.1=py38h3c74f83_1
+  - idna=2.10=py_0
+  - ld_impl_linux-64=2.33.1=h53a641e_7
+  - libedit=3.1.20191231=h14c3975_1
+  - libffi=3.3=he6710b0_2
+  - libgcc-ng=9.1.0=hdf63c60_0
+  - libstdcxx-ng=9.1.0=hdf63c60_0
+  - ncurses=6.2=he6710b0_1
+  - openssl=1.1.1h=h7b6447c_0
+  - pip=20.2.4=py38h06a4308_0
+  - pycosat=0.6.3=py38h7b6447c_1
+  - pycparser=2.20=py_2
+  - pyopenssl=19.1.0=pyhd3eb1b0_1
+  - pysocks=1.7.1=py38h06a4308_0
+  - python=3.8.5=h7579374_1
+  - readline=8.0=h7b6447c_0
+  - requests=2.24.0=py_0
+  - ruamel_yaml=0.15.87=py38h7b6447c_1
+  - setuptools=50.3.1=py38h06a4308_1
+  - six=1.15.0=py38h06a4308_0
+  - sqlite=3.33.0=h62c20be_0
+  - tk=8.6.10=hbc83047_0
+  - tqdm=4.51.0=pyhd3eb1b0_0
+  - urllib3=1.25.11=py_0
+  - wheel=0.35.1=pyhd3eb1b0_0
+  - xz=5.2.5=h7b6447c_0
+  - yaml=0.2.5=h7b6447c_0
+  - zlib=1.2.11=h7b6447c_3
+prefix: /home/cermak/miniconda3

conda/bokeh.yml

@@ -0,0 +1,14 @@
+name: bokeh
+# This is a bokeh/jupyterlab specific environment
+channels:
+  - conda-forge
+dependencies:
+  - bokeh
+  - jupyter_bokeh
+  - cartopy
+  - geopandas
+  - xlrd
+  - openpyxl
+  - jupyterlab
+  - conda
+  - pip