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‎.gitignore

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‎README.md

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# gridtools
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A collection of grid generation tools
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A generic set of grid manipulation tools for computer models. These tools are
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adapted from the ROMS ocean model and for specific use in the MOM6 ocean model.
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One could hope it can be kept generic enough to support any model. The focus
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is on supporting the MOM6 ocean model.
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For in depth details about the MOM6 ocean model, please visit provided
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[wiki](https://github.com/NOAA-GFDL/MOM6-examples/wiki) pages. Technical
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details about this repository can be found below. For usage of
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the GridUtils library, please visit the [user manual](docs/manual/GridUtils.md).
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Required items:
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* spherical.py
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* gridutils.py
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* app.py
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Optional items:
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* sysinfo.py
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Various tools are available to manipulation of new and existing grids in
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an iterative or interactive form.
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Python notebooks:
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* mkGridIterative.ipynb
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* mkGridInteractive.ipynb
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With this software, you should be able to operate in any mode you prefer.
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# Operational Modes
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## Command Line
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Using the command line or writing your own python scripts possible utilizing this library.
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To look at a few examples, please look at the mkGridsExample1.py, mkGridsExample2.py and
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mkGridsExample3.py programs.
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## Command Line Widget Mode
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* ipython --pylab
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The interpreter, ipython, can run python scripts and notebook scripts. To run a notebook
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script, you can use `ipython -c "%run your_script.ipynb"`. Or start ipython, and then
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`%run your_script.ipynb`.
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Again, the mkGridsExample.py programs can be run with ipython.
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## Jupyter notebook
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* jupyter notebook
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These prefer notebook files (ipynb). Please see the mkGridIterative.ipynb program for a hands
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on way to access the grid generation library.
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A simple graphical user interface (GUI) was built and is available when you run the
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mkGridInteractive.ipynb notebook.
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## Jupyter lab
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* jupyter lab
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These prefer notebook files (ipynb). Please see the mkGridIterative.ipynb program for a hands
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on way to access the grid generation library.
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A simple graphical user interface (GUI) was built and is available when you run the
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mkGridInteractive.ipynb notebook.
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## mybinder
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* Main: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ESMG/gridtools/main)
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* Dev: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ESMG/gridtools/dev)
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Instead of loading software on your computer, the library and application is hosted on a cloud system. You do not
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have to install anything on your system to use the cloud system's copy of the grid generation library.
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# Application
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The grid generation application, mkGridInteractive.ipynb, can be run on a cloud hosting system. The application has been adapted to work on mybinder.org.
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NOTICE: The mybinder application can take upwards to 30 minutes to build.
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Use the following options:
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* GitHub=https://github.com/ESMG/gridtools
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* Git ref=main
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* Launch
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* Once the server loads, navigate to gridTools/mkMapInteractive.ipynb
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* Re-run all the cells
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* Have fun with the grid editor.
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# Code contributions
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## Lambert Conformal Conic Grid Generation
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Author: Niki Zadeh [REPO](https://github.com/nikizadehgfdl/grid_generation)
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* [regional_grid_spheical.ipynb](https://github.com/nikizadehgfdl/grid_generation/blob/dev/jupynotebooks/regional_grid_spherical.ipynb)
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## Numpy bitwise-the-same floating-point values
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Author: Alistair Adcroft [REPO](https://github.com/adcroft/numpypi)
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* To obtain bitwise-the-same floating-point values in certain non-time-critical calculations.
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## ROMS to MOM6 Grid Converter
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Authors: Mehmet Ilicak; Alistair Adcroft [REPO](https://github.com/ESMG/pyroms)
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* [convert_ROMS_grid_to_MOM6.py](https://raw.githubusercontent.com/ESMG/pyroms/python3/examples/grid_MOM6/convert_ROMS_grid_to_MOM6.py)
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# Installation
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If you plan to use the grid generation software on your system, you need to peform the following steps.
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## Step 1
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[Download](https://github.com/ESMG/gridtools/archive/refs/heads/main.zip) or [clone](https://github.com/ESMG/gridtools.git) the
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[ESMG/gridtools](https://github.com/ESMG/gridtools) repository.
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Discover the full directory path to gridtools/gridTools/lib. Place the full path in the environment variable `LIBROOT` if you are planning to run
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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
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installation using ptyhon pip.
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## Step 2
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Install conda or manually install the python libraries and software dependencies that would allow you to run the python scripts or notebooks.
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We have pulled together some pre-defined environments. You may also install an environment yourself. Please look at the [conda](docs/conda/README.md)
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page for more information about conda.
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We currently recommend the *xesmfTools* environment for use with this libaray.
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## Step 3
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Follow any steps in the "Workarounds" section.
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# Workarounds
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These are the current workarounds that are required for the grid toolset
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package. You will need to perform these steps once if you plan to install a
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copy of the grid generation software.
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## datashader
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The lastest version from github is required for proper operation of bokeh, holoviews and panel which
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are used by the interactive portions of the grid generation library.
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[REPO](https://github.com/holoviz/datashader)
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Installation:
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* Download or clone this repository.
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* Change directory to the datashader directory.
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* Make sure your conda enviroment is active.
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* `pip install -e .`
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## numpypi
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NOTE: This has not been fully implemented yet. Do not worry about this just yet.
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For bitwise-the-same reproducable results, a numpy subset of computational functions are
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provided. These routines are slower than the numpy native routines.
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[REPO](https://github.com/adcroft/numpypi)
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# More
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Until we can activate Sphinx to create our body of documentation we will have to resort
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to upkeep of a manual index.
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[Documentation](docs/Documentation.md)
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* [conda](docs/conda/README.md)
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* [development](docs/development)
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* [CHANGELOG](docs/development/CHANGELOG.md): Development log of changes
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* [CREDITS](docs/development/CREDITS.md)
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* [Design](docs/development/Design.md): Design elements for the grid generation library
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* [Important References](docs/development/ImportantReferences.md): Things that helped this project work
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* [Jupyter](docs/development/Jupyter.md): Notes on embeddeding applications within a notebook
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* [python](docs/development/python)
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* [leaflet](docs/development/python/leaflet.md)
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* [panel](docs/development/python/panel.md)
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* [pyroms](docs/development/python/pyroms.md)
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* [TODO](docs/development/TODO.md): Milestones, tasks, todos and wishes
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* [grids](docs/grids)
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* [Examples](docs/grids/Examples.md): Descriptions of grids used in examples
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* [Grids](docs/grids/Grids.md)
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* [MOM6](docs/grids/MOM6.md): MOM6 grids
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* [MOM6ROMS](docs/grids/MOM6ROMS.md): Important things between MOM6 and ROMS grids
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* [ROMS](docs/grids/ROMS.md): ROMS grids
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* [manual](docs/manual/GridUtils.md): User manual for the GridUtils library
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* [resources](docs/resources)
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* [Bathymetry](docs/resources/Bathymetry)
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# Development
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This project is soliciting help in development. Please contribute ideas or bug requests using the issues tab.
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Code contributions can be sent via github's pull request process.

‎conda/base_export.yml

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

‎conda/bokeh.yml

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name: bokeh
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# This is a bokeh/jupyterlab specific environment
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channels:
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- conda-forge
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dependencies:
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- bokeh
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- jupyter_bokeh
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- cartopy
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- geopandas
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- xlrd
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- openpyxl
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- jupyterlab
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- conda
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- pip

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