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Streamline getting started documentation #636
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version: 3.12.0rc3 | ||
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+++ {"editable": true, "slideshow": {"slide_type": ""}, "tags": []} | ||
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# Exploring the Virtual Ecosystem outputs | ||
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The code below provides a walkthrough of some basic plots for the input and output of the Virtual Ecosystem simulation. | ||
The code below provides a walkthrough of some basic plots for the input and output of | ||
the Virtual Ecosystem simulation. | ||
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## Run the simulation | ||
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Before exploring the outputs you will need to run the simulation using the example data or your own input data. If you have already run the simulation and generated outtput data, you can skip to the [Initial state and input data](#initial-state-and-input-data) section below. | ||
Before exploring the outputs you will need to run the simulation using the example data | ||
or your own input data. If you have already run the simulation and generated outtput | ||
data, you can skip to the | ||
[Initial state and input data](#initial-state-and-input-data) section below. | ||
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The following commands allow you to run the simulation from a Jupyter Notebook. However, you can also run the script from the command line following the [Getting Started](getting_started.md) instructions. | ||
The following commands allow you to run the simulation from a Jupyter Notebook. | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. It is great to remind the users that they can run the python codes using Jupyter Notebook. However, I struggle to even comprehend where to type the following commands after launching Jupyter Notebook, sorry! Most ecologists or biologists would be more familiar with R than python, so it would be a shame to turn them away because we didn't ease them into python. That said, I struggle between providing too much details about python coding here (some users may already know how and find it boring) versus hand-carrying new users. Should we dedicate a new page just for using python codes in Jupyter, or at least point the users to an external tutorial page? |
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However, you can also run the script from the command line following the [Getting | ||
Started](getting_started.md) instructions. | ||
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```{code-cell} ipython3 | ||
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Even though one could just remove the files using file explorer, should we give an example code to remove the files (e.g., using
rm
) for those who have little experience with the Terminal?If so, probably write it after the
ve_run
chunk for a better flow...There was a problem hiding this comment.
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In the other file I just realised that @jacobcook1995 had already written something, maybe ditto them here for completeness?
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I think it's generally not great practice to use bash scripts to delete directories, because you might end up deleting something by mistake. It's useful in that example because the files are being stored in a kind of weird location (in the user directory) which might be hard to find using Finder. But I personally would encourage users to keep the data files in the
virtual_ecosystem
directory, because they will likely need to access them while working, and it will all stay a lot more organized that way. That is why I used this method - and in addition, I just think it overcomplicates the task to run a bash script, when the files should be easy to find.Let me know what you think about that reasoning!!
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All good. I agree that it is unnecessary :) The only thing left to decide if whether to list the filenames to be deleted, but this is not always the same (e.g., the initial states may not be saved depending on user setting.) When I first bumped into this I had to ask around which files to remove.