Update Ubuntu install instructions for 2020 fall #56

joelostblom · 2020-07-24T18:26:06Z

I am making this a draft because I am adding a few comments to the changes, will ping when ready for review.

- `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

… in jupyterlab

…ble there

The verification is already mentioned on the linked page

resources_pages/install_ds_stack_ubuntu.md

joelostblom · 2020-07-24T19:00:18Z

resources_pages/install_ds_stack_ubuntu.md


 ```
 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"


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.

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.

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 · 2020-07-24T19:03:38Z

@ttimbers Ready for review! I have gone through everything except Chrome and LastPass instructions. ~~Also it seems like I can't assign people to review, I might need different permissions on this repo.~~ (my bad, I had not accepted your invite to the team)

resources_pages/install_ds_stack_ubuntu.md

joelostblom · 2020-07-25T18:29:47Z

Just confirmed that chrome and lastpass instructions are correct.

resources_pages/install_ds_stack_ubuntu.md

ttimbers

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.

resources_pages/install_ds_stack_ubuntu.md

ttimbers · 2020-07-28T05:28:28Z

resources_pages/install_ds_stack_ubuntu.md

-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:


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.

Agree, updated.

Great, thanks!

ttimbers · 2020-07-28T05:29:59Z

resources_pages/install_ds_stack_ubuntu.md


 ```
-install.packages(c('tidyverse', 'tinytex', 'blogdown', 'xaringan', 'renv'))
+install.packages(c('tidyverse', 'tinytex', 'blogdown', 'xaringan', 'renv', 'IRkernel'))


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).

Suggested change

install.packages(c('tidyverse', 'tinytex', 'blogdown', 'xaringan', 'renv', 'IRkernel'))

install.packages(c('tidyverse', 'blogdown', 'xaringan', 'renv', 'IRkernel'))

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.

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

joelostblom

@ttimbers Thanks for the review, see my replies here!

resources_pages/install_ds_stack_ubuntu.md

joelostblom · 2020-07-28T15:54:33Z

resources_pages/install_ds_stack_ubuntu.md

-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:


Agree, updated.

resources_pages/install_ds_stack_ubuntu.md

joelostblom · 2020-07-28T16:08:28Z

resources_pages/install_ds_stack_ubuntu.md


 ```
-install.packages(c('tidyverse', 'tinytex', 'blogdown', 'xaringan', 'renv'))
+install.packages(c('tidyverse', 'tinytex', 'blogdown', 'xaringan', 'renv', 'IRkernel'))


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.

joelostblom · 2020-07-28T16:17:07Z

resources_pages/install_ds_stack_ubuntu.md


 ```
 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"


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).

resources_pages/install_ds_stack_ubuntu.md

ttimbers · 2020-07-28T20:15:34Z

@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.

joelostblom

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.

resources_pages/install_ds_stack_ubuntu.md

ttimbers · 2020-07-29T05:24:26Z

@joelostblom - I think the one thing left to do is to pull out the IRkernel package install as discussed above (conceptually this makes more sense even though its a bit more work).

joelostblom · 2020-07-29T05:55:05Z

@ttimbers I did do this in 7aaba85, or are we referring to different things?

ttimbers · 2020-07-29T05:56:47Z

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!

joelostblom · 2020-07-29T05:58:20Z

Great! I will start with the win instructions tomorrow, making similar changes as what we agreed upon here.

ttimbers · 2020-07-29T05:59:18Z

Before you move onto that - can you bring the relevant changes we made to ubuntu back to mac?

joelostblom · 2020-07-29T06:04:53Z

Yes, sorry forgot that we said that when I wrote above, I'll do that first tomorrow morning.

joelostblom added 13 commits July 23, 2020 09:33

Emphasize note about windows version

2066606

Fix typos

db8362d

Simplify slack, vscode, and github instructions

6c6e630

Remove duplicated github instructions

383b484

Clarify git instructions

e4f63e6

Clarify python and conda instructions

4f47e4e

Simplify R install instructions

7bae059

- `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

Clarify RStudio installation instruction and update screenshot

9c4759f

Clarify and remove duplicated instructions for the IRkernel section

4d73df8

Clarify latex instructions and add note on how to test PDF generation…

aee45fd

… in jupyterlab

Install postgres from the default repo since version 12 is now availa…

e24c460

…ble there

Remove duplicated latex instructions

df0faf4

Shorten docker instructions

641894d

The verification is already mentioned on the linked page

joelostblom commented Jul 24, 2020

View reviewed changes

Consolidate spacing after headings

ce5b9d1

joelostblom marked this pull request as ready for review July 24, 2020 19:02

joelostblom commented Jul 24, 2020

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joelostblom self-assigned this Jul 24, 2020

joelostblom requested a review from ttimbers July 24, 2020 22:02

joelostblom removed their assignment Jul 24, 2020

Consolidate notes on chrome and rstudio installations

a000cb2

ttimbers reviewed Jul 28, 2020

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ttimbers requested changes Jul 28, 2020

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joelostblom added 2 commits July 27, 2020 23:43

Add image of ubuntu Rstudio

2d3e739

Missed this in the previous commit

Update according to Tiffany's review

c29d873

- 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

joelostblom commented Jul 28, 2020

View reviewed changes

Add notes about ubuntu and conda install

4d907ea

joelostblom added 3 commits July 28, 2020 21:17

Clarify linked sections

6f95909

Recommend rstudio preview

7b77d53

Move IRkernel install to its own section

7aaba85

joelostblom commented Jul 29, 2020

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ttimbers merged commit cdaf793 into UBC-MDS:master Jul 29, 2020

joelostblom mentioned this pull request Jul 29, 2020

Mac os install 2020 #61

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Update Ubuntu install instructions for 2020 fall #56

Update Ubuntu install instructions for 2020 fall #56

joelostblom commented Jul 24, 2020

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	install.packages(c('tidyverse', 'tinytex', 'blogdown', 'xaringan', 'renv', 'IRkernel'))
	install.packages(c('tidyverse', 'blogdown', 'xaringan', 'renv', 'IRkernel'))

Update Ubuntu install instructions for 2020 fall #56

Update Ubuntu install instructions for 2020 fall #56

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