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Update Ubuntu install instructions for 2020 fall #56
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- `apt update` happens automatically after adding a new repo - Multiple packages can be installed on the same line - Note removed since I clarified in the intro blurb
The verification is already mentioned on the linked page
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``` | ||
install.packages('tinytex') | ||
tinytex::install_tinytex() | ||
``` | ||
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The above is all we need to have LaTeX work with R Markdown documents, however to for Jupyter we need to add the TinyTex executables to our `PATH` and install several more packages. | ||
The above is all we need to have LaTeX work with R Markdown documents, however to for Jupyter we need to add the TinyTex executables to our `PATH` and install several more packages. | ||
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To add the TinyTex executables to our `PATH` we need to edit our `.bashrc` file. The TinyTex executables are usually installed in `$HOME/bin`. Thus, add the lines below to the bottom of your `.bashrc` file (which you can open by `code $HOME/.bashrc`): | ||
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``` | ||
# add TinyTex executables to the path | ||
export PATH="$HOME/bin:$PATH" |
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Is it safe to prepend this directory or should we append it instead? I don't know what is higher risk, unwanted executables in this dir that get unwanted preference over other system packages, or unintentional addition of latex packages to other path dirs that get preference over tinyTex unless it is first.
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Sure, change it to append instead (assuming it still works, which it should). I wondered that as I was doing it...
Also, can you confirm that after these LaTeX install instructions you can create PDFs from Jupyter? I see you do this later.
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Yup works fine, updated the instructions. I also added this brief explanation of what PATH
is (maybe slightly technically inprecise but helpful at this point):
(
PATH
is a collection of directories which contain the available executable programs on your computer).
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Great!
@ttimbers Ready for review! I have gone through everything except Chrome and LastPass instructions. |
Just confirmed that chrome and lastpass instructions are correct. |
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There were a few other comments I made before officially starting this review (sorry), so please read through all my comments that I posted tonight in addition to these. Then ping me when done and I will accept the PR.
We will be using several Jupyter extensions that help us use Juypter notebooks more smoothly with Git & GitHub. To install them, paste the following in the terminal below: | ||
## JupyterLab extensions | ||
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We will be using a couple of JupyterLab git extensions to facilitate using Jupyter notebooks with Git & GitHub. Install them via the following commands: |
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These are not all git extensions technically. Jupytext is kind of like nbconvert on steriods. So I would prefer to not refer to all of these as git extensions.
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Agree, updated.
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Great, thanks!
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``` | ||
install.packages(c('tidyverse', 'tinytex', 'blogdown', 'xaringan', 'renv')) | ||
install.packages(c('tidyverse', 'tinytex', 'blogdown', 'xaringan', 'renv', 'IRkernel')) |
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Let's remove tinytex
here and just install it later under the LaTeX section, as I think this logically makes more sense (as they need another command to install it as well).
install.packages(c('tidyverse', 'tinytex', 'blogdown', 'xaringan', 'renv', 'IRkernel')) | |
install.packages(c('tidyverse', 'blogdown', 'xaringan', 'renv', 'IRkernel')) |
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Ok, do you want me to also move back IRkernel
to it's own section? I thought it would be nice to just have to run install.packages
once, but I also see the value in having each heading being largely self-contained.
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Yeah maybe... I think conceptually it makes sense so folks know what the individual things are for (tinyTex for LaTeX, IRkernel for the R kernel for Jupyter, and the rest are R packages for other stuff).
Missed this in the previous commit
- Update Github link - Indicate that jupytext is not a jupyterlab extension - Clarify R version numbers - Note how RStudio updates - Remove duplicate install of tiny tex - Append instead of repend to path
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@ttimbers Thanks for the review, see my replies here!
We will be using several Jupyter extensions that help us use Juypter notebooks more smoothly with Git & GitHub. To install them, paste the following in the terminal below: | ||
## JupyterLab extensions | ||
|
||
We will be using a couple of JupyterLab git extensions to facilitate using Jupyter notebooks with Git & GitHub. Install them via the following commands: |
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Agree, updated.
|
||
``` | ||
install.packages(c('tidyverse', 'tinytex', 'blogdown', 'xaringan', 'renv')) | ||
install.packages(c('tidyverse', 'tinytex', 'blogdown', 'xaringan', 'renv', 'IRkernel')) |
There was a problem hiding this comment.
Choose a reason for hiding this comment
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Ok, do you want me to also move back IRkernel
to it's own section? I thought it would be nice to just have to run install.packages
once, but I also see the value in having each heading being largely self-contained.
|
||
``` | ||
install.packages('tinytex') | ||
tinytex::install_tinytex() | ||
``` | ||
|
||
The above is all we need to have LaTeX work with R Markdown documents, however to for Jupyter we need to add the TinyTex executables to our `PATH` and install several more packages. | ||
The above is all we need to have LaTeX work with R Markdown documents, however to for Jupyter we need to add the TinyTex executables to our `PATH` and install several more packages. | ||
|
||
To add the TinyTex executables to our `PATH` we need to edit our `.bashrc` file. The TinyTex executables are usually installed in `$HOME/bin`. Thus, add the lines below to the bottom of your `.bashrc` file (which you can open by `code $HOME/.bashrc`): | ||
|
||
``` | ||
# add TinyTex executables to the path | ||
export PATH="$HOME/bin:$PATH" |
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Yup works fine, updated the instructions. I also added this brief explanation of what PATH
is (maybe slightly technically inprecise but helpful at this point):
(
PATH
is a collection of directories which contain the available executable programs on your computer).
@joelostblom - I have just gone through your review response and made a few more comments. Once you go through these and address them, ping me and I'll call this done and merge it. |
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Should be good to merge now @ttimbers. I will attend your office hours tomorrow also in case we need to discuss something about this quickly before merging.
@joelostblom - I think the one thing left to do is to pull out the |
Sorry, that is perfect, I must have clicked on a different commit and saw that it wasn't done. Apologies! Looks good and I will merge now! |
Great! I will start with the win instructions tomorrow, making similar changes as what we agreed upon here. |
Before you move onto that - can you bring the relevant changes we made to ubuntu back to mac? |
Yes, sorry forgot that we said that when I wrote above, I'll do that first tomorrow morning. |
I am making this a draft because I am adding a few comments to the changes, will ping when ready for review.