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Add instructions for actually running the tutorials to intro.html #119

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hyanwong opened this issue Jul 13, 2021 · 0 comments · Fixed by #120
Closed

Add instructions for actually running the tutorials to intro.html #119

hyanwong opened this issue Jul 13, 2021 · 0 comments · Fixed by #120

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@hyanwong
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hyanwong commented Jul 13, 2021

We should make it easy for a tutee to copy and paste the code cells in most of the tutorials to their own Jupyter notebooks (especially the basics/getting_started ones), and for it to work the majority of the time. For this we need to give them instructions about what they need to install.

One possibility is e.g. to expose requirements.txt to a general location and in intro.html recommend something like

pip install -r https://tskit.dev/tutorials/requirements.txt

Although this would install jupyterbook, which is not actually needed to run the code cells. To run the R stuff we also need the tutee to run R -e 'install.packages(c("reticulate", "IRkernel")); IRkernel::installspec()' as described in the GitHub repo README file.

Also, basically the first code line in basics.html is ts = tskit.load("data/basics.trees") which won't work if copied and pasted, so this is a prime candidate for loading from a URL (see #116 & tskit-dev/tskit#1566)

hyanwong added a commit to hyanwong/tutorials that referenced this issue Jul 16, 2021
hyanwong added a commit to hyanwong/tutorials that referenced this issue Jul 16, 2021
hyanwong added a commit to hyanwong/tutorials that referenced this issue Jul 16, 2021
hyanwong added a commit to hyanwong/tutorials that referenced this issue Jul 16, 2021
hyanwong added a commit to hyanwong/tutorials that referenced this issue Jul 16, 2021
hyanwong added a commit to hyanwong/tutorials that referenced this issue Jul 16, 2021
hyanwong added a commit to hyanwong/tutorials that referenced this issue Jul 16, 2021
hyanwong added a commit to hyanwong/tutorials that referenced this issue Jul 16, 2021
hyanwong added a commit to hyanwong/tutorials that referenced this issue Jul 19, 2021
hyanwong added a commit to hyanwong/tutorials that referenced this issue Jul 20, 2021
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