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Extract remaining citations #1687

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Nov 21, 2020
Merged

Extract remaining citations #1687

merged 1 commit into from
Nov 21, 2020

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charleskawczynski
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@charleskawczynski charleskawczynski commented Nov 2, 2020 •
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Description

Extracts remaining references/citations to docs/bibliography.bib.

  • Code follows the style guidelines OR N/A.
  • Unit tests are included OR N/A.
  • Code is exercised in an integration test OR N/A.
  • Documentation has been added/updated OR N/A.

@trontrytel
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This is great. However I think there is something wrong in how the References page is rendered. The entries are listed based on the labels given to them in the code and not by the first author name or year.

Also, before this change, clicking on the links in my docs would lead to the relevant paper available on the journal page. Now it just leads to the References page. And the links in the Reference page are placed weirdly and in general lead back to the References page and not the paper.

@charleskawczynski
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However I think there is something wrong in how the References page is rendered.

I agree that it doesn't look great right now, but I think we can improve things in DocumenterCitations.jl and the reference page will eventually look better as we upgrade.

The entries are listed based on the labels given to them in the code and not by the first author name or year.

I'm not sure I understand. Can you give an example?

Also, before this change, clicking on the links in my docs would lead to the relevant paper available on the journal page. Now it just leads to the References page. And the links in the Reference page are placed weirdly and in general lead back to the References page and not the paper.

That's a good point. Ideally, each entry would be placed inside an HTML tag with an active attribute so that when someone clicks on one of the references, it could activate the HTML attribute so that the entry is highlighted. I think that this is something that can also be improved on the DocumenterCitations.jl side.

@trontrytel
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The entries are listed based on the labels given to them in the code and not by the first author name or year.

I'm not sure I understand. Can you give an example?

Screenshot 2020-11-02 at 09 25 11

@trontrytel
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Also, before this change, clicking on the links in my docs would lead to the relevant paper available on the journal page. Now it just leads to the References page. And the links in the Reference page are placed weirdly and in general lead back to the References page and not the paper.

That's a good point. Ideally, each entry would be placed inside an HTML tag with an active attribute so that when someone clicks on one of the references, it could activate the HTML attribute so that the entry is highlighted. I think that this is something that can also be improved on the DocumenterCitations.jl side.

I'm not sure I understand. My point is that it's way more useful for the links to point to the actual paper than to a reference list based on which you have to find the paper.

@simonbyrne simonbyrne mentioned this pull request Nov 2, 2020
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@charleskawczynski
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charleskawczynski commented Nov 2, 2020 •
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I'm not sure I understand. My point is that it's way more useful for the links to point to the actual paper than to a reference list based on which you have to find the paper.

Wouldn't it still be useful if we included direct links to the paper in the reference entry? Right now they're broken (and there are obviously formatting issues), but that's a DocumenterCitation problem. I think that navigating citations would be very easy between including direct links and highlighting the clicked entry.

@trontrytel
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I'm not sure I understand. My point is that it's way more useful for the links to point to the actual paper than to a reference list based on which you have to find the paper.

Wouldn't it still be useful if we included direct links to the paper in the reference entry? Right now they're broken (and there are obviously formatting issues), but that's a DocumenterCitation problem. I think that navigating citations would be very easy between including direct links and highlighting the clicked entry.

I agree. If the links in the reference page work I'm fine with it.

I guess we want the reference page to safeguard against when the link stops working and you still want to be able to find the paper by yourself.

@charleskawczynski
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I guess we want the reference page to safeguard against when the link stops working and you still want to be able to find the paper by yourself.

That's a good point, we should make sure that Documenter still checks the links after References.md has been generated.

@jkozdon
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jkozdon commented Nov 2, 2020 •
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We should make sure we use doi numbers and doi links when possible, this will safeguard against links breaking.

(I don't see any dois listed in the references page, can we add that?)

@charleskawczynski
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I don't see any dois listed in the references page, can we add that?

Yes, most of the refs I grabbed were from Google Scholar, but not all of them had doi links, so we'll need a second pass to add them where possible.

@simonbyrne
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The links are based on the doi when it is available. We should add them to the bibtex entries.

@jkozdon
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jkozdon commented Nov 2, 2020

The links are based on the doi when it is available. We should add them to the bibtex entries.

I see that now. I just didn't mouse over the ones that were.

@charleskawczynski
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bump

@trontrytel
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trontrytel commented Nov 9, 2020 •
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bump

Are the links pointing to the actual papers working now in the docs? Some of them seem to work, but most do not.

Having to chose between a) having links that work in the text b) having a reference list without links working I would chose option a.

@trontrytel
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Also, the references are still not sorted in any order?

@charleskawczynski
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Are the links pointing to the actual papers working now in the docs? Some of them seem to work, but most do not.

Ahh, I can see that not all entries I used included URLs, I'll go and fix the ones that we previously had.

Also, the references are still not sorted in any order?

No, IMO, that's a problem that we can ship off for DocumenterCitations to solve-- and we should be able to fix it through an upgrade to a newer version which solves this problem.

@trontrytel
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Are the links pointing to the actual papers working now in the docs? Some of them seem to work, but most do not.

Ahh, I can see that not all entries I used included URLs, I'll go and fix the ones that we previously had.

Also, the references are still not sorted in any order?

No, IMO, that's a problem that we can ship off for DocumenterCitations to solve-- and we should be able to fix it through an upgrade to a newer version which solves this problem.

Sounds good. IMHO I don't care about formatting of the reference list. But I think that links should end up pointing to papers

@charleskawczynski
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Updated.

@trontrytel
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Looks like now it's timing out?

@charleskawczynski
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Looks like now it's timing out?

I think I just haven't tried rebuilding now that the docs are run on the cluster

@charleskawczynski charleskawczynski force-pushed the ck/extract_refs branch 2 times, most recently from 215d0ed to 2ab70dc Compare November 19, 2020 15:51
@charleskawczynski
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Bump

@simonbyrne
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Thanks!

@trontrytel
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For me the links in the references are still mostly not working. So in my book it's change for worse. But if everyone else disagrees, please merge

@charleskawczynski
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For me the links in the references are still mostly not working. So in my book it's change for worse. But if everyone else disagrees, please merge

Which link(s)?

@simonbyrne
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https://clima.github.io/ClimateMachine.jl/previews/PR1687/References/#Smagorinsky1963

@trontrytel
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For me the links in the references are still mostly not working. So in my book it's change for worse. But if everyone else disagrees, please merge

Which link(s)?

For example the first two Toro2013 and Rutledge1983 entries have links that for me point back to the reference page

@charleskawczynski
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Ok, I think the links that point to the references page can be fixed upstream.

The smagorinsky entry is wrong, I see that I accidentally copied entries of Lilly model and put them into the Smagorinsky model. I’ll fix that tomorrow.

Perhaps we can merge after that and we can try to tackle some of the upstream issues (I’ll make sure to open an upstream issue regarding the links that aren’t working).

@charleskawczynski
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Thanks for reviewing!

@charleskawczynski
Extract remaining citations
d667797 
Extract remaining citations

Extract more citations, polish format
@charleskawczynski
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bors r+

bors bot added a commit that referenced this pull request Nov 20, 2020
@bors @charleskawczynski
Merge #1687 #1725
ca84348 
1687: Extract remaining citations r=charleskawczynski a=charleskawczynski

### Description

Extracts remaining references/citations to `docs/bibliography.bib`.



1725: Move first order moisture flux to new tendency specification r=charleskawczynski a=charleskawczynski

### Description

This PR

 - moves the first order moisture flux to the new tendency specification. I can confirm that the tendency table is updated, for `experiments/AtmosLES/bomex_model.jl` with `moisture_model == "nonequilibrium"`, but I haven't checked the results.
 - Renames `flux_moisture!` to `flux_first_order!` in efforts to standardize some of the AtmosModel method calls
 - Adds `Moisture <: PrognosticVariable` to combine specification for the moisture variables.




Co-authored-by: Charles Kawczynski <kawczynski.charles@gmail.com>
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bors bot commented Nov 20, 2020

Build failed (retrying...):

bors bot added a commit that referenced this pull request Nov 20, 2020
@bors @charleskawczynski
Merge #1687
1770b0a 
1687: Extract remaining citations r=charleskawczynski a=charleskawczynski

### Description

Extracts remaining references/citations to `docs/bibliography.bib`.



Co-authored-by: Charles Kawczynski <kawczynski.charles@gmail.com>
bors bot added a commit that referenced this pull request Nov 20, 2020
@bors @charleskawczynski
Merge #1687
1c498cc 
1687: Extract remaining citations r=charleskawczynski a=charleskawczynski

### Description

Extracts remaining references/citations to `docs/bibliography.bib`.



Co-authored-by: Charles Kawczynski <kawczynski.charles@gmail.com>
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bors r+

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bors bot commented Nov 21, 2020

Build succeeded:

@bors bors bot merged commit 3524f8f into master Nov 21, 2020
@bors bors bot deleted the ck/extract_refs branch November 21, 2020 00:10
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@simonbyrne simonbyrne simonbyrne approved these changes

@trontrytel trontrytel Awaiting requested review from trontrytel

@thomasgibson thomasgibson Awaiting requested review from thomasgibson

@glwagner glwagner Awaiting requested review from glwagner

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@charleskawczynski @trontrytel @jkozdon @simonbyrne