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<p>Okay. I will put efforts in that direction. That will be easier.<br>
</p>
<div class="moz-cite-prefix">On 1/16/24 13:01, Jose Duarte wrote:<br>
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<blockquote type="cite"
cite="mid:CAHhO=JFJELdcz_HeMv7b+aCHWkcMJSyg46ffBgF2sa6Z5bgMZw@mail.gmail.com">
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<div dir="ltr">Just want to confirm that the preferred way to
write documentation for BioJava is through the tutorial github
site that Peter points out: <a
href="https://github.com/biojava/biojava-tutorial"
moz-do-not-send="true" class="moz-txt-link-freetext">https://github.com/biojava/biojava-tutorial</a>
<div><br>
</div>
<div>The docs and tutorials in <a href="http://github.io"
moz-do-not-send="true">github.io</a> are quite outdated and
came from migrating the previous wiki. It really needs a good
clean up. </div>
<div><br>
<div>Jose</div>
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<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Mon, 15 Jan 2024 at 08:39,
Gary Murphy <<a href="mailto:hilbertglm@gmail.com"
moz-do-not-send="true" class="moz-txt-link-freetext">hilbertglm@gmail.com</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Yes
replying to you only was in error. I will take a look at the
Python <br>
project you mentioned. I also got the Jekyll code going by
regressing <br>
to a previous version.<br>
<br>
Thanks again for the feedback.<br>
<br>
<br>
On 1/15/24 10:19, Peter Cock wrote:<br>
> Whoops - I missed that as I initially assumed hilberglm
was<br>
> someone else. Sorry. By the way, I'm happy to take this
thread<br>
> back to the mailing list if replying to just me was in
error.<br>
><br>
> In Biopython we use a tool called blacken-docs to apply
the same<br>
> automated formatting style (defined in a tool called
black) to the<br>
> examples in our documentation that we use in the main
code:<br>
><br>
> <a href="https://pypi.org/project/blacken-docs/"
rel="noreferrer" target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">https://pypi.org/project/blacken-docs/</a><br>
><br>
> I don't know if there is something similar possible in
Java?<br>
><br>
> As to the automated builds with Jekyll, there are likely
some<br>
> fixes made on <a
href="https://github.com/biopython/biopython.github.io/"
rel="noreferrer" target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">https://github.com/biopython/biopython.github.io/</a><br>
> which can be copied over.<br>
><br>
> Peter<br>
><br>
> On Mon, Jan 15, 2024 at 4:06 PM Gary Murphy <<a
href="mailto:hilbertglm@gmail.com" target="_blank"
moz-do-not-send="true" class="moz-txt-link-freetext">hilbertglm@gmail.com</a>>
wrote:<br>
>> Thank you for getting back to me so quickly. Yes, I
am the Gary Murphy<br>
>> that forked the source to take a look at it and
understand how to build<br>
>> it. I should have posted the official github URL
instead of my fork.<br>
>><br>
>> I have some code that reads FASTA files using Java
streams that I<br>
>> haven't submitted a pull request for, but I wanted to
have a handle on<br>
>> how to document it if it was accepted. Specifically,<br>
>> _wiki/BioJava_CookBook_Core_FastaReadWrite.md is the
one I updated<br>
>> locally, but haven't pushed. I also noted a lot of
formatting errors on<br>
>> the source code in the Cookbook, so I would be
changing those only when<br>
>> I update a page... a global update would be pretty
time-consuming.<br>
>><br>
>> More generally, since I am learning the code base, I
thought it would be<br>
>> beneficial for me to add documentation when I learn
how to do things in<br>
>> the normal course of my job that I had to jump into
the source code<br>
>> and/or test cases to understand.<br>
>><br>
>> The first thing I would be updating is how to update
the documentation.<br>
>> The Jekyll docker container is broken out of the
gate, so I had to<br>
>> figure out how to get the build server running
locally to ensure my<br>
>> changes were getting rendered properly.<br>
>><br>
>> I have spent some time in the tutorials. They are
extremely helpful and<br>
>> seem to be more recently updated.<br>
>><br>
>><br>
>> On 1/15/24 09:49, Peter Cock wrote:<br>
>>> I'd guess the source you want is <a
href="https://github.com/biojava/biojava.github.io"
rel="noreferrer" target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">https://github.com/biojava/biojava.github.io</a><br>
>>> but Gary Murphy's version <a
href="https://github.com/hilbertglm/biojava.github.io.git"
rel="noreferrer" target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">https://github.com/hilbertglm/biojava.github.io.git</a><br>
>>> looks to be the same right now - this is the main
BioJava website and<br>
>>> it does indeed look not to have been updated
recently. This includes what<br>
>>> used to be the wiki content (including the
cookbook), now as markdown pages.<br>
>>> This repository also includes API documentation.<br>
>>><br>
>>> What specifically did you want to change here?
e.g. An example URL<br>
>>><br>
>>> See also <a
href="https://github.com/biojava/biojava-tutorial"
rel="noreferrer" target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">https://github.com/biojava/biojava-tutorial</a>
which has been changed<br>
>>> much more recently.<br>
>>><br>
>>> Peter<br>
>>><br>
>>> On Mon, Jan 15, 2024 at 2:53 PM Gary Murphy <<a
href="mailto:hilbertglm@gmail.com" target="_blank"
moz-do-not-send="true" class="moz-txt-link-freetext">hilbertglm@gmail.com</a>>
wrote:<br>
>>>> Sorry if this is a duplicate, but the mailing
list confirmation got moved to the spam folder, so I don't
know if this original e-mail was honored.<br>
>>>><br>
>>>> -----<br>
>>>><br>
>>>> I am new to the biojava community, so I
thought I would be a good candidate to update some of the
documentation as I discover how to accomplish my goals with
biojava.<br>
>>>><br>
>>>> I got the source for the Cookbook (<a
href="https://github.com/hilbertglm/biojava.github.io.git"
rel="noreferrer" target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">https://github.com/hilbertglm/biojava.github.io.git</a>),
and it seems like it is a bit out of date with quite a few
formatting issues for the source code.<br>
>>>><br>
>>>> Before I start...<br>
>>>><br>
>>>> Is there any effort I should be aware of for
a new one, or is anyone actively working on it? If so, we
should coordinate efforts<br>
>>>> Does anyone have any issue with my removing
the non-breaking spaces in the source code. It shows as
[NBSP] in Intellij, so it is going to be tough to do any
editing on that.<br>
>>>><br>
>>>> Any thoughts would be appreciated.<br>
>>>><br>
>>>>
_______________________________________________<br>
>>>> Biojava-l mailing list - <a
href="mailto:Biojava-l@biojava.org" target="_blank"
moz-do-not-send="true" class="moz-txt-link-freetext">Biojava-l@biojava.org</a><br>
>>>> <a
href="https://mailman.open-bio.org/mailman/listinfo/biojava-l"
rel="noreferrer" target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">https://mailman.open-bio.org/mailman/listinfo/biojava-l</a><br>
>>> _______________________________________________<br>
>>> Biojava-l mailing list - <a
href="mailto:Biojava-l@biojava.org" target="_blank"
moz-do-not-send="true" class="moz-txt-link-freetext">Biojava-l@biojava.org</a><br>
>>> <a
href="https://mailman.open-bio.org/mailman/listinfo/biojava-l"
rel="noreferrer" target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">https://mailman.open-bio.org/mailman/listinfo/biojava-l</a><br>
_______________________________________________<br>
Biojava-l mailing list - <a
href="mailto:Biojava-l@biojava.org" target="_blank"
moz-do-not-send="true" class="moz-txt-link-freetext">Biojava-l@biojava.org</a><br>
<a
href="https://mailman.open-bio.org/mailman/listinfo/biojava-l"
rel="noreferrer" target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">https://mailman.open-bio.org/mailman/listinfo/biojava-l</a><br>
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