Reproduce skeleton with updates

[Schiano-NOAA]

What is the feature?

• Create new feature to re-render the skeleton after create_template is initially ran without overwriting other files -- this will be a temporary way to produce this feature. In the future, the goal is to allow the user to run create_template(rerender_skeleton=TRUE) in the console and make the changes in a simple, efficient way

How have you implemented the solution?

• Added a new argument to create_template
• Modularized create_template further

Does the PR impact any other area of the project, maybe another repo?

[sbreitbart-NOAA]

Can you please provide an example for how to use the new rerender_skeleton argument? I've been trying this and it's not producing a skeleton qmd with an updated species name in my original report folder (./report) nor the new report folder created in the original report folder (./report/report):

create_template(rerender_skeleton = TRUE, species = "Black sea bass", file_dir = "report")

[Schiano-NOAA]

Can you please provide an example for how to use the new rerender_skeleton argument? I've been trying this and it's not producing a skeleton qmd with an updated species name in my original report folder (./report) nor the new report folder created in the original report folder (./report/report):

create_template(rerender_skeleton = TRUE, species = "Black sea bass", file_dir = "report")

I haven't added in an example because I feel like there are already a lot of examples in the script.

The way to use this feature is to run create_template(rerender_skeleton = TRUE, ...) you can select one of the arguments described in the documentation for now such as adding in a new section, changing the sectioning, updating the model output file name, adding an additional bibliography, adding more authors, and more. The caveat is that that working directory should be the "report" folder where the skeleton.qmd is located. The arguments in your example won't change anything. The argument assumes that you still want to use the same script and folder, but just update the skeleton with a few options (even though they could just be updated manually as well)

[sbreitbart-NOAA]

Can you please provide an example for how to use the new rerender_skeleton argument? I've been trying this and it's not producing a skeleton qmd with an updated species name in my original report folder (./report) nor the new report folder created in the original report folder (./report/report):
create_template(rerender_skeleton = TRUE, species = "Black sea bass", file_dir = "report")

I haven't added in an example because I feel like there are already a lot of examples in the script.

The way to use this feature is to run create_template(rerender_skeleton = TRUE, ...) you can select one of the arguments described in the documentation for now such as adding in a new section, changing the sectioning, updating the model output file name, adding an additional bibliography, adding more authors, and more. The caveat is that that working directory should be the "report" folder where the skeleton.qmd is located. The arguments in your example won't change anything. The argument assumes that you still want to use the same script and folder, but just update the skeleton with a few options (even though they could just be updated manually as well)

I keep running into issues. For instance, I'll enter the basic create_template(), then set the wd to "report", then enter asar::create_template(rerender_skeleton =T, alt_title = T, title = "my new title", office = "NWFSC", species = "new fish", new_section = "my_new_section", section_location = "after-introduction"). The skeleton qmd file is updated, but with the "{{< pagebreak >}} Please cite this publication as: " and output_and_quantities section repeated over and over.

[Schiano-NOAA]

Okay that’s super odd. I will try and fix this. The argument will inherit the old region so you should not have to replace that. I did not however set it up to update a completely blank template so I need to do that. If you want to add a new section, custom = T needs to be added to the arguments still. Thanks for your testing!

…

On Fri, Mar 7, 2025 at 11:09 AM Sophie Breitbart ***@***.***> wrote: Can you please provide an example for how to use the new rerender_skeleton argument? I've been trying this and it's not producing a skeleton qmd with an updated species name in my original report folder (./report) nor the new report folder created in the original report folder (./report/report): create_template(rerender_skeleton = TRUE, species = "Black sea bass", file_dir = "report") I haven't added in an example because I feel like there are already a lot of examples in the script. The way to use this feature is to run create_template(rerender_skeleton = TRUE, ...) you can select one of the arguments described in the documentation for now such as adding in a new section, changing the sectioning, updating the model output file name, adding an additional bibliography, adding more authors, and more. The caveat is that that working directory should be the "report" folder where the skeleton.qmd is located. The arguments in your example won't change anything. The argument assumes that you still want to use the same script and folder, but just update the skeleton with a few options (even though they could just be updated manually as well) I keep running into issues. For instance, I'll enter the basic create_template(), then set the wd to "report", then enter asar::create_template(rerender_skeleton =T, alt_title = T, title = "my new title", office = "NWFSC", species = "new fish", new_section = "my_new_section", section_location = "after-introduction"). The skeleton qmd file is updated, but with the "{{< pagebreak >}} Please cite this publication as: " and output_and_quantities section repeated over and over. — Reply to this email directly, view it on GitHub <#160 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A55RLSRZCJZPOIFSG26PZ7D2THADJAVCNFSM6AAAAABWSDOGP6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDOMBWHA2TAMBSGU> . You are receiving this because you authored the thread.Message ID: ***@***.***> [image: sbreitbart-NOAA]*sbreitbart-NOAA* left a comment (nmfs-ost/asar#160) <#160 (comment)> Can you please provide an example for how to use the new rerender_skeleton argument? I've been trying this and it's not producing a skeleton qmd with an updated species name in my original report folder (./report) nor the new report folder created in the original report folder (./report/report): create_template(rerender_skeleton = TRUE, species = "Black sea bass", file_dir = "report") I haven't added in an example because I feel like there are already a lot of examples in the script. The way to use this feature is to run create_template(rerender_skeleton = TRUE, ...) you can select one of the arguments described in the documentation for now such as adding in a new section, changing the sectioning, updating the model output file name, adding an additional bibliography, adding more authors, and more. The caveat is that that working directory should be the "report" folder where the skeleton.qmd is located. The arguments in your example won't change anything. The argument assumes that you still want to use the same script and folder, but just update the skeleton with a few options (even though they could just be updated manually as well) I keep running into issues. For instance, I'll enter the basic create_template(), then set the wd to "report", then enter asar::create_template(rerender_skeleton =T, alt_title = T, title = "my new title", office = "NWFSC", species = "new fish", new_section = "my_new_section", section_location = "after-introduction"). The skeleton qmd file is updated, but with the "{{< pagebreak >}} Please cite this publication as: " and output_and_quantities section repeated over and over. — Reply to this email directly, view it on GitHub <#160 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A55RLSRZCJZPOIFSG26PZ7D2THADJAVCNFSM6AAAAABWSDOGP6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDOMBWHA2TAMBSGU> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[Schiano-NOAA]

@sbreitbart-NOAA I just pushed a fix to the issue. By repeating the species and other params parameters, it breaks the code for the yaml (good catch!). The code should now run as intended.
One thing I will note: you do not need to repeat any other arguments in the function. When rerendering the skeleton, you just need to run create_template(rerender_skeleton = TRUE...) then only add arguments for the things you want to change. While either way works, the other way is simpler and easier to follow.

Great- now the first example works. With the second, it either repeats the initial 3 authors and then adds the new one (when run as in my initial example), or if I remove the author argument, it now adds an "NA" author before my new one (Sun E Day). I think showing some examples of how someone might use this argument would be really useful here since I have shown multiple ways to use it incorrectly, or at least not in the intended way.

I can make a fix so it check to make sure authors are not repeated if someone happens to use the same code as before with just the new argument. My intention is that this approach to using create_template(rerender_skeleton=TRUE) is that users can just run in in the console to make quick adjustments/improvements

[Schiano-NOAA]

@sbreitbart-NOAA Can you rerun your example and let me know if you have any other issues?

[sbreitbart-NOAA]

Minor note: the .Rd documentation needs updating (this doesn't appear in that file)

[sbreitbart-NOAA]

@sbreitbart-NOAA Can you rerun your example and let me know if you have any other issues?

If I run this code:

create_template(model_results = "converted_file_1126.csv",
                year = 2020,
                species = "Petrale sole",
                type = "SAR",
                prev_year = 2019,
                model = "SS3",
                author = c("John Snow", "Danny Phantom", "Patrick Star"),
                resdir = here::here(),
                rda_dir = here::here(),
                recruitment_unit_label = "mt",
                end_year = 2022,
                n_projected_years = 10,
                relative = FALSE,
                ref_line = "unfished",
                ref_point = 13000,
                landings_unit_label = "mt",
                spawning_biomass_label = "mt",
                ref_line_sb = "msy",
                ref_point_sb = 2000,
                indices_unit_label = "CPUE",
                biomass_unit_label = "mt",
                catch_unit_label = "mt")

setwd("report")

create_template(add_author = c("Sophie Breitbart"),
               rerender_skeleton = TRUE)

I get a skeleton.qmd file that still has an 'NA' before the newly added author:

[Schiano-NOAA]

@sbreitbart-NOAA I am not getting that. Have you pulled down the changed from online?

[sbreitbart-NOAA]

@sbreitbart-NOAA I am not getting that. Have you pulled down the changed from online?

Yes, I've fetched and rebased multiple times, and closed/reopened RStudio. Not sure what the issue is! If you're not getting it, then maybe it's not an issue?