Added the option to import from Github

[Vitalis95]

Fixes #8823
@lilyclements @rdstern @N-thony , Added the option (R package -button) to install a package directly from GitHub

[rdstern]

@lilyclements could you check that this is ok. I notice that the github option does not have the check facility. @Vitalis95 Isn't that still needed, when adding from github?

[lilyclements]

@Vitalis95 - this is great! There's one comment given in the R code, then two other bits below:

1. We discussed last week about having a check, but I did a little bit of coding today and was able to sort it out. Can you add the following function into the "stand_alone_functions.R" file:

# Function to check if a repo exists and is in R 
check_github_repo <- function(owner, repo) {
  tryCatch({
    response <- gh::gh("/repos/:owner/:repo", owner = owner, repo = repo, verb = "GET", silent = TRUE)
    if (response$language == "R") {
      return(1)  # Repository exists and is in the R language
    } else {
      return(2)  # Repository exists, but isn't in the R language
    }
  }, error = function(e) {
    return(3)  # Error occurred, repository doesn't exist
  })
}

Then we want to add for the messages something like this:

         Case "1"
                ucrInputMessage.SetText("Package exists in the repo and is ready for installation")
                ucrInputMessage.txtInput.BackColor = Color.LightGreen
            Case "2"
                ucrInputMessage.SetText("Package exists in the repo but is not in the R language")
                ucrInputMessage.txtInput.BackColor = Color.LightGreen
          Case "3"
                ucrInputMessage.SetText("Not a package in the given repo. Perhaps spelled wrongly?")
                ucrInputMessage.txtInput.BackColor = Color.LightCoral

2. Can you add as a new argument in the function upgrade = "never". This can be hardcoded in.

Otherwise looks good!

[lilyclements]

You don't need your paste function here since you've already combined it with your code! So you can just change this to

clsRepositoryFunction.AddParameter("paste", Chr(34) & ucrInputRepositoryName.GetText & "/" & ucrInputTextBoxRPackage.GetText & Chr(34), bIncludeArgumentName:=False)

And then you can remove the bit on line 180, and remove clsPasteFunction entirely :)

[Vitalis95]

@lilyclements , have a look at it

[lilyclements]

@Vitalis95 this is nice that you've removed the paste0 function, and worked on that.

There's a few changes with the check needed for the GitHub option.

My previous comment gave a function as well as suggestions to the code to amend for this check. Does it make sense to you? It's ok if not, I do need to work on my explanations!

Then another point is that I noticed the tab order is out. Can you sort this as well?

[Vitalis95]

@lilyclements , I've fixed the tab order , I'm researching how we can further enhance the suggestions you provided

[Vitalis95]

@lilyclements , have a look at this

[lilyclements]

This is good - I have tidied up the design a little bit, so before you make further changes then make sure that you pull the most recent changes. If you don't agree with the changes, we can revert the commit (it's very minor bits of aligning etc).

I can't see the addition of the check_github_repo function that I mentioned above though? Is this added in another PR?

[Vitalis95]

@lilyclements , I have added check_github_repo function

[lilyclements]

@Vitalis95 this is good. Just one small thing - is it possible for the OK to be disabled if the check fails (i.e., is in red). This is done elsewhere - like when checking unique in the dlgKeys dialog, if you want to look at the code?

[Vitalis95]

@lilyclements , have a look at it

[rdstern]

@lilyclements and @Vitalis95 this looks like a nice enhancement. I had a quick look, partly to check that the Help button works, which it does.
I couldn't then test, because I don't have any examples to try. I should check the issue in more detail first perhaps. Is there at least one that you have in mind, that we could include in the Help information?

I wonder also if the repository name field should be wider than the package name? It is a URL and likely to be quite long? Are there any examples that we know we may use? If so, then could this be a drop down, where you can paste a new url, but there are (say) a couple of obvious examples?

[lilyclements]

@rdstern some examples from various R packages we've developed at IDEMS:

Repo: IDEMSInternational
Package: rpicsa, epicsawrap, cdms.products, carbonr, rapidpror, openappr, networkGraphsR, instatExtras

[rdstern]

Great. How about that repo and sone, or all, those examples in a drop down. The default is still blank, (so the user types or pastes the contents) but this would give at least one example where no typing is needed? And we could use that in the help on how to do this.

[Vitalis95]

Great. How about that repo and sone, or all, those examples in a drop down. The default is still blank, (so the user types or pastes the contents) but this would give at least one example where no typing is needed? And we could use that in the help on how to do this.

@lilyclements , what do you think about this?

[lilyclements]

@Vitalis95 I think this is a good idea, but, perhaps I'm a little late with my response. If I'm too late then ignore me!

[Vitalis95]

@lilyclements @rdstern , I have added IDEMSInternational as repo and a drop down with above packages, the default is blank

[N-thony]

@lilyclements @rdstern , I have added IDEMSInternational as repo and a drop down with above packages, the default is blank

@lilyclements @rdstern can you re-test this?

[N-thony]

@rdstern over to you

[rdstern]

@Vitalis95 and @lilyclements I am not quite sure what is expected here?

a) I first tried with each of the packages in the drop-down menu:

This goes green - they all go green. (So I assume none as currently installed, or are not the most current version?)

So I installed the first package. I assume it installed.

Then I tried again and it still was green. Shouldn't it now say the package is already installed?

Some of the options it says are not R packages - but they are still green. What does that mean? I take green to mean I should install it. Can I install a not R package?

b) Then I tried with a climatic package - CDT that is also only in Github? I could not get it so I could install? I first assumed I could find the whole directory and copy it over. Then I got rid of the start as shown below. Am I supposed to be able to install this sort of package or just our own?

(Note the instructions are i9n the CDT github directory and they work in the script window. So is this dialog only meant for the IDEMSInternational packages?)

c) Finally I returned to your packages in the drop-down menu. Now I don't know the location any more. I can get it back, by pressing Reset and then going back to the Github. So not a real problem. But couldn't it also give that directory when I choose from the dropdown?

[lilyclements]

@rdstern thanks for this review. There are certainly changes in the R code that you have highlighted here. I have worked on these, so let me know what you think:

Installing New Packages
To import "rijaf-iri/CDT", then you would put "rijaf-iri" in the Repo Name, and "CDT" in the package name.

This is really great to see how it can be interpreted - perhaps we should have two options: One where you import from a URL, and one like how we have it now?

• Import from URL - if this is an option, then we just have one input box where the user writes in the URL.
• Import from ?? - if this selected, then we have it as it is at the moment.

It is very straightforward to do this in R, so I have added it as an option in the R code for now. We don't have to put this in the dialog if you disagree - good to get opinions though @rdstern or @Vitalis95 - what do you think?

Adding more options when importing from GitHub - I've done this on the checks now
Our check_github_repo() function now returns 0-6 depending on the reason (I've done it numerically as I think this is easier for Vitalis when coding it his end. If not then I can easily amend it!

Return	Text/Reason to put in Dialog	Colour in Dialog?	Explanation
0	Package is up to date	Orange?	OK does not need to be enabled here - this occurs if the package is installed and up to date, so there is no need to reinstall.
1	Package exists in the repo and is ready for installation	Green	OK can be enabled! We can install the R package as we are updating it
2	Unable to retrieve from GitHub. Check internet connection?	Red	OK cannot be enabled due to issue with server.
3	Package exists in the repo and is ready for installation	Green	OK can be enabled! We can install the R package as we are updating it.
4	Package exists in the repo and is ready for installation	Green	OK can be enabled! We can install the R package as we are installing it for the first time.
5	Package exists but is not in the R language	Red	Do not enable OK
6	Not a package in the given repo. Check spelling?	Red	Do not enable OK

@rdstern @Vitalis95 what are your thoughts on this? Hopefully makes it a bit easier for the user if they encounter issues when installing.

# Examples working my end which you may wish to use (Note: These may give different results your end, especially for the first two!)

check_github_repo(url = "https://github.com/rijaf-iri/CDT")  # This gives a 0 for me since I have installed it and it's up to date. If you've installed this one and it's up to date you should get a 0. 
check_github_repo(url = "https://github.com/IDEMSInternational/openappr")  # This gives a 1 for me since I have installed it but not the latest version.
check_github_repo(url = "https://github.com/IDEMSInternational/openappr")  # If you switch off your internet, you can get a 2.
check_github_repo(url = "https://github.com/tidyverse/dplyr") # 3 Package is installed but not from GitHub - because we've installed this one from CRAN
check_github_repo(url = "https://github.com/simonpcouch/anyflights") # Assuming you haven't installed this (I picked a random one!), you should get a 4 because the repo exists and is in the R language
check_github_repo(url = "https://github.com/mvuorre/exampleRPackage") # Assuming you haven't installed this (I picked a random one!), you should get a 4 because the repo exists but is not in the R language
check_github_repo(url = "https://github.com/rijaf-iri/CDT2")  # You should get a 6 because I made this one up.

[rdstern]

@lilyclements that's great:
a) Tried CDT and it installed fine. It also confirmed how many packages we have that are out-of date!
b) But when I tried it again it was still green and with the same message. With CRAN packages it would now say it was installed?

c) However with (at least some of) the IDEMS packages the Check doesn't work now. It doesn't give anything now for Rpicsa or epicsawrap::

d) With CDMS Products (and carbonr and openappr) it gives the wrong message - I know it isn't a CRAN package!

e) With carbonr and rapidpror is gives the following incorrect message!

[rdstern]

I am musing now. Suppose we rewrite R-Instat to use the 3 main R packages that you have just documented. (You bravely said that might be a boring but feasible job for one of our programmers???!)
Then if occasionally, a small update, was to one of these packages only, then that could be updated this way and would not need everything to be updated to a whole new version?

[lilyclements]

@rdstern glad that (a) is now working.
To (b)-(e) apologies I wasn't clear enough - I've shared the R code for this, but the VB code on the dialog needs to be updated still.
(I changed some of the numbers in this new updated function since we've added in more options. So currently your warnings are misspecified until we update the dialog VB code! I forgot I did this, I'm sorry for the confusion there)

[lilyclements]

@rdstern @Vitalis95 I just, I hope, updated the VB code to reflect the new options of 0-6 in this dialog. If you try again, it should hopefully work now!

I haven't done any other bits (like, adding a URL option, if we wanted that)

[lilyclements]

I am musing now. Suppose we rewrite R-Instat to use the 3 main R packages that you have just documented. (You bravely said that might be a boring but feasible job for one of our programmers???!)
Then if occasionally, a small update, was to one of these packages only, then that could be updated this way and would not need everything to be updated to a whole new version?

@rdstern good point! This could be a great "easy" way to get this done

[rdstern]

@lilyclements that's great. All the options in your pull down now work and give useful messages. This is all very nice.

I don't think we need the option of the url. The insalling of packages, like CDT works fine.

The only item remaining is to check on packages like CDT and to give the installed message when it is there.

Then let's merge.

[rdstern]

@lilyclements I now noticed that as well as importing a package it now seems to check and list all the other packages in R-Instat that are out-of date. That's new and I wonder if it will worry users unnecessarily?

We usually update the packages with successive releases. So gradually they will become not the most recent. But that is not usually a problem for the user?

[Vitalis95]

@rdstern , have a look at it.

[rdstern]

@Vitalis95 I don't see what's different?

I had 2 minor problems before: and they are still here
a) After installing CDT (example of a github package, when I try again it is still green. I would like it to detect it is installed and tell me.
b) It gives me a (worrying) list of all the installed packages that are out of date. I don't really want that and used not to get it when installing CRAN packages.

[lilyclements]

@Vitalis95 is there a reason you changed the colours to be Red/Green instead of LightCoral, etc? Just out of interest

[lilyclements]

@rdstern to (a), this is very interesting since I am not having this problem. There is some coding going on with checking your version vs the version on GitHub, but perhaps the check we need to do is slightly different between our computers. I think this is something to investigate "in person" - we can set as an issue for now?

To (b), this is something that comes up in R from the code. We can remove this by adding upgrade = "never" as a parameter, e.g.

devtools::install_github("IDEMSInternational/openappr", upgrade = "never")

I've added this in @Vitalis95. If you make any other changes, make sure you pull this branch first (sorry for interfering -- just know you have a lot to do and it's a one-line bit I can actually do!).
@rdstern point (b) is hopefully fixed now?

[rdstern]

@lilyclements it now doesn't show the out-of-date packages.
It still shows CDT to be installed always, but you say that might be a machine issue.
Anyway I am accepting, because Chris and @N-thony have now changed the "system", so all the packages on installation continue to be in the original directory, while all we install with this dialog, go into a second directory - and R-Instat looks there first!

I am keen to use this new dialog, in the new version to test all this. I also often have problems updateing some CRAN packages, because R-Instat loads them at the start. We perhaps need a list of those so we don't try to update, them, or learn how that is done. @N-thony perhaps you can supply this list, so we can include it in the help?

@N-thony over to you to check and merge. Really good to have this in the forthcoming release.

[lilyclements]

@Vitalis95 thanks for changing the colours. Very minor, but very appreciated! I'll approve since @rdstern was happy with it before this minor change and this commit made his approval stale.

@N-thony over to you to check and merge

PS: Might help if I actually click "Approve" this time (hence the removed comment above)