USER settings have no effect

[andy941]

USER settings have no effect

[cmhughes]

Thanks for this, no trouble at all :)

Have you tried using the m switch, as in

latexindent.pl -m tmp/tmp.tex

See also https://latexindentpl.readthedocs.io/en/latest/sec-the-m-switch.html#lst-tw-bf-myenv1

[andy941]

Thanks for the quick answer!

I confirm that it works with the -m flag on the minimal example I gave. For some reason it doesn't work when I do the same on a longer, more complicated file. There are special cases.
This is a good example from the thesis I'm writing:

\textit{AP1}'s expression pattern follows \textit{LFY}, but with a slightly
delayed timing~\cite{AlejandraMandel1992}. The loss of function mutant \textit{ap1} forms
a high number of ectopic flowers resulting in an increased inflorescence branching.
Sepals are rarely seen in \textit{ap1} mutants and petals are homeotically
transformed into sepal-like organs, from which, at the axels, new \textit{ap1}
flowers develop displaying the same phenotype~\cite{Mandel1995}. Constitutive expression of
\textit{AP1} under the \textit{CaMV 35S} promoter causes early flowering
shoots, a phenotype that resembles a \textit{tfl1} mutant~\cite{Mandel1995}.

AP1 and LFY act in concert to
promote the floral transition
but interestingly, LFY
promotes TFL1 expression when
AP1 is not present, revealing
another layer of complexity
that is still largely
unfathomed~\cite{Goslin2017}.

In this case I used the command latexindent -m -y="modifyLineBreaks:textWrapOptions:columns:30" nanopore_rnaseq.tex to get rid of any prblems that may arise from the settings in the yaml config.
The problem seems to be something else, maybe \textit{} is messing up with latexindent? It might recognize the whole block (between the blank lines) as a function and skip indentation?
Should I change something like blocksBeginWith?

[cmhughes]

Great! Yep, blocks begin with should help. See the following example https://latexindentpl.readthedocs.io/en/latest/sec-the-m-switch.html#lst-tw-bb-announce1

…

On Tue, 10 May 2022, 15:35 andy941, ***@***.***> wrote: Thanks for the quick answer! I confirm that it works with the -m flag on the minimal example I gave. For some reason it doesn't work when I do the same on a longer, more complicated file. There are special cases. This is a good example from the thesis I'm writing: \textit{AP1}'s expression pattern follows \textit{LFY}, but with a slightly delayed timing~\cite{AlejandraMandel1992}. The loss of function mutant \textit{ap1} forms a high number of ectopic flowers resulting in an increased inflorescence branching. Sepals are rarely seen in \textit{ap1} mutants and petals are homeotically transformed into sepal-like organs, from which, at the axels, new \textit{ap1} flowers develop displaying the same phenotype~\cite{Mandel1995}. Constitutive expression of\textit{AP1} under the \textit{CaMV 35S} promoter causes early flowering shoots, a phenotype that resembles a \textit{tfl1} mutant~\cite{Mandel1995}. AP1 and LFY act in concert to promote the floral transition but interestingly, LFY promotes TFL1 expression when AP1 is not present, revealing another layer of complexity that is still largely unfathomed~\cite{Goslin2017}. In this case I used the command latexindent -m -y="modifyLineBreaks:textWrapOptions:columns:30" nanopore_rnaseq.tex to get rid of any prblems that may arise from the settings in the yaml config. The problem seems to be something else, maybe \textit{} is messing up with latexindent? It might recognize the whole block (between the blank lines) as a function and skip indentation? Should I change something like blocksBeginWith? — Reply to this email directly, view it on GitHub <#362 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAQ7CYGUTF6P2XX2RY6HKZTVJJX3HANCNFSM5VRI3V4Q> . You are receiving this because you commented.Message ID: ***@***.***>

[andy941]

Yes I was thinking about that option, just wanted to make sure there wasn't anything easier I was missing. It works well now thanks, it's surprisingly helpful to work with well formatted text (I am a latex newbie).
Thanks for the help!

[cmhughes]

Great to hear :) If you feel like posting the yaml that works for you, do feel free to share in case it can help others :) no worries if not. Happy latexing!

…

On Tue, 10 May 2022, 16:59 andy941, ***@***.***> wrote: Closed #362 <#362>. — Reply to this email directly, view it on GitHub <#362 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAQ7CYHSVI3HBP3DSKIPKNLVJKBXDANCNFSM5VRI3V4Q> . You are receiving this because you commented.Message ID: ***@***.***>

[andy941]

Sure, I was just worried that this would be a very inelegant regex (it has not been "tested"):

modifyLineBreaks:
    textWrapOptions:
        columns: 79
        blocksBeginWith:
            other: '\\text[a-z]*\{.*\}'

I wanted to handle all the \text* like \textbf for example, however the * could be substituted with something more specific. There is still the problem that \textit{aaa ... aaa} gets a hard indent (tab) no matter what when the break is inside the {}. I can live with that anyway, it's just nitpicking at that point.

Thanks again, hopefully this can help others in the future.

[cmhughes]

Nice, thanks for sharing. I'd use *? so that it's not greedy :) Happy TeXing!

…

On Tue, 10 May 2022, 18:18 andy941, ***@***.***> wrote: Sure, I was just worried that this would be a very elegant regex (it has not been "tested"): modifyLineBreaks: textWrapOptions: columns: 79 blocksBeginWith: other: '\\text[a-z]*\{.*\}' I wanted to handle all the \text* like \textbf for example, however the * could be substituted with something more specific. There is still the problem that \textit{aaa ... aaa} gets a hard indent (tab) no matter what when the break is inside the {}. I can live with that anyway, it's just nitpicking at that point. Thanks again, hopefully this can help others in the future. — Reply to this email directly, view it on GitHub <#362 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAQ7CYFMXNEOLICLJN6VTALVJKK7PANCNFSM5VRI3V4Q> . You are receiving this because you commented.Message ID: ***@***.***>