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update README.md, Manifest.toml, & re-name as MarineEcosystemNotebooks (#3)
* update and improve README; re-name as MarineEcosystemNotebooks * update Manifest.toml
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‎Manifest.toml

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# This file is machine-generated - editing it directly is not advised
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‎README.md

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# Cbiomes2019Notebooks
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# MarineEcosystemNotebooks
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[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/gaelforget/Cbiomes2019Notebooks/master)
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[![DOI](https://zenodo.org/badge/185446209.svg)](https://zenodo.org/badge/latestdoi/185446209)
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The `Notebooks/` folder illustrate:
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[Jupyter](https://jupyter.org) notebooks related to marine ecosystem models and observations in [Julia](https://julialang.org).
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1. how ocean colour data and model ouptut can be used jointly in [CBIOMES](https://cbiomes.org)
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2. how [Simons' CMAP](https://cmap.readthedocs.io/en/latest/) can be queried from within `julia` or `python` via [pycmap](https://github.com/simonscmap/pycmap)
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1. how ocean colour data and model ouptut can be used jointly in [CBIOMES](https://https://github.com/CBIOMES)
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2. how the [Simons' CMAP](https://cmap.readthedocs.io/en/latest/) database can be queried from within `julia`.
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<p align="center">
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<img width="600" src="https://raw.githubusercontent.com/gaelforget/Cbiomes2019Notebooks/master/figs/cbiomes-01.png">
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<img width="300" src="https://raw.githubusercontent.com/gaelforget/Cbiomes2019Notebooks/master/figs/cbiomes-01.png">
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</p>
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_Notes:_
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- To start an interactive version of the notebooks, please click on the `launch binder` badge.
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- Included notebooks are written in the [Julia](https://julialang.org) language.
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- Notebooks are paired with corresponding `.jl file` that run directly in `julia`.
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- The `src/` folder contains `julia` utility scripts.
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- _Each `.ipynb` notebook is paired with a `.jl` file via `jupytext`_
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- _An interactive version can readily be spun up via the `launch binder` badge_
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- _Please use the [repository issue tracker](https://guides.github.com/features/issues/) for queries, bug reports, new contributions, etc._
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- _The `src/` folder contains helper functions & scripts._
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## Ocean color
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## Ocean Color
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- `01. OceanColourAlgorithms.ipynb` provides simple recipes to compare [CBIOMES model output](https://github.com/gaelforget/CBIOMES) and [ocean color data](https://www.oceancolour.org).
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- `02. ModelReflectanceMap.ipynb` uses `Plots.jl` to map out [CBIOMES model output](https://github.com/gaelforget/CBIOMES) and [ocean color data](https://www.oceancolour.org).
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- `05. OceanColourClassifiers.ipynb` 2D array demo of [OC-CCI](https://www.oceancolour.org) / [Jackson et al 2017](http://doi.org/10.1016/j.rse.2017.03.036) classifier.
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## Query CMAP
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## Data Bases
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- `03. DarwinCmapJulia.ipynb` uses [Simons' CMAP](https://cmap.readthedocs.io/en/latest/) to download output of the [CBIOMES model output](https://github.com/gaelforget/CBIOMES) as a file or dataframe using `julia`'s `pycall` package to call the `pycmap` python package.
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- `04. DarwinCmapPython.ipynb` uses [Simons' CMAP](https://cmap.readthedocs.io/en/latest/) to map output of the Darwin model using the `pycmap` python package (this is a **python rather than julia** notebook).

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