List of things to fix/adjust before issue 1 published (we will ask for people to redo the templates then).

[mrshirts]

1. Sometimes, the link to the GitHub repository in the PDF isn't working. See https://www.livecomsjournal.org/article/5965-introduction-to-markov-state-modeling-with-the-pyemma-software-article-v1-0
2. Figure out ORCID iD placement.

[mrshirts]

Add to the above as we go.

[dwsideriusNIST]

1. Sometimes, the link to the GitHub repository in the PDF isn't working. See https://www.livecomsjournal.org/article/5965-introduction-to-markov-state-modeling-with-the-pyemma-software-article-v1-0

Author forgot the "https://" prefix in the \github macro. Do we want to modify the macro to add a missing prefix, or just check it manually?

[dwsideriusNIST]

2. Figure out ORCID iD placement.

-> Bringing text in from https://github.com/livecomsjournal/livecomsjournal.github.io/pull/173

I made a slight revision to the CLS file to create the ORCID block. Results are visible here: https://github.com/dmzuckerman/Sampling-Uncertainty/blob/orcid/main.pdf, page 22

The ORCIDs are input via a macro function, e.g.:

\orcid{Daniel W. Siderius}{https://orcid.org/}{0000-0002-6260-7727} \orcid{Daniel M. Zuckerman}{https://orcid.org/}{0000-0001-7662-2031}

Ideally, I would like argument 1 to reference the author name from the \author function, but I haven't been able figure out how to access that variable in the main CLS file. Help?

[davidlmobley]

If we can auto-add the https:// prefix that'd certainly be a time-saver.

[dwsideriusNIST]

If we can auto-add the https:// prefix that'd certainly be a time-saver.

Upon revisiting the macro... it's not a macro, just a variable definition in the manuscript preamble. We can make it a macro if you really want to go down that road.

[davidlmobley]

Not sure how difficult that is. If it's easy, then I'd go for it but if it's going to take a pretty significant investment of time then I'd just make sure we check this...

In other words, how quick is the return on investment?

[davidlmobley]

@mrshirts can you not use the "assigned" tab unless the person is actually going to DO it and has agreed to do so? Sometimes I use the "assigned" thing as a tasks list for myself.

It works better, if you want feedback on something, to just tag me in the issue tracker (or if it is a PR, request a review from me). But in my mind "assigned" means a very specific thing: I'm the one responsible for completing the referenced task.

[mrshirts]

@davidlmobley OK sounds good.

[dwsideriusNIST]

Not sure how difficult that is. If it's easy, then I'd go for it but if it's going to take a pretty significant investment of time then I'd just make sure we check this...

In other words, how quick is the return on investment?

I came up with a quick macro that adds the URL prefix to a github repo name if it is missing, but then realized that it would be about impossible to error check all the ways an author could garble the URL by entering the repo name incorrectly. Ultimately, the repo name has to be typed correctly, which is no different than just entering the URL properly in the first place. Thus, I would vote for no macro, just the preamble variable definition.

[davidlmobley]

Sounds good.

[dwsideriusNIST]

OK, thanks, I'll put in a PR to the pyEMMA paper with a fix to their github URL

[mrshirts]

Or let them do it. They are aware now.

[dwsideriusNIST]

PR is already in, it's doing an automatic circleCI check.

[dwsideriusNIST]

Is the ACS-style ORCID list OK for you all? I can settle on the formatting if you're happy with it.

@davidlmobley put out a request to @liantze to see if we can make the orcid macro more sophisticated, otherwise the macro just include duplicate info. (https://github.com/livecomsjournal/livecomsjournal.github.io/pull/173)

As for alternative author IDs, I wrote the macro in a way that it could be repurposed for other author IDs in case that is ever needed.

[dmzuckerman]

I'm OK with what @dwsideriusNIST has done. If we can get something fancier in time, that would be nice, but the main thing is to have the numbers.

[dwsideriusNIST]

OK, I'll put in a PR with the simple macro and updates to the templates. We can change the livecoms class file in the future if we figure out how to pull author names directly from the \author macros. It won't change the output, just the macro syntax.

At some point we'll need authors of the already-published papers to update their CLS and BST files, then recompile.

[dwsideriusNIST]

See PR #71

[dwsideriusNIST]

This is an attempt to triage the remaining to-do items for the template:

1a. Approve final form of footer; specifying "ASAP" or actual citation info. 1b. Author instructions for activating the publication footer

2a. Finalize Author identifiers / ORCID. Based on PR https://github.com/livecomsjournal/livecomsjournal.github.io/pull/173 for the github.io site, it seems that a simple macro is best at present. PR #71 provides working code 2b. Author instructions

3. Finalize guidelines for versioning. See https://github.com/livecomsjournal/livecomsjournal.github.io/issues/176

[davidlmobley]

I agree with that ordering, @dwsideriusNIST .

[dwsideriusNIST]

OK, watch for a sequence of PRs to address these items.

[dwsideriusNIST]

In need of opinion: The instructions for both the "pubversion"/"ASAPversion" class options and the ORCID identifier should be in the templates repo itself, right? I think those instructions are too specific for the github.io site, so I'm thinking of adding them to

https://github.com/livecomsjournal/article_templates/blob/master/information_for_authors.md

(BTW, that markdown file needs some reorganization as well.) OR... should there be a specific page about class options.

[dwsideriusNIST]

See PR #72

[dwsideriusNIST]

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