[Biojava-l] Updating the Cookbook (Resend)

[Gary Murphy]

Yes replying to you only was in error.  I will take a look at the Python 
project you mentioned.  I also got the Jekyll code going by regressing 
to a previous version.

Thanks again for the feedback.


On 1/15/24 10:19, Peter Cock wrote:
> Whoops - I missed that as I initially assumed hilberglm was
> someone else. Sorry. By the way, I'm happy to take this thread
> back to the mailing list if replying to just me was in error.
>
> In Biopython we use a tool called blacken-docs to apply the same
> automated formatting style (defined in a tool called black) to the
> examples in our documentation that we use in the main code:
>
> https://pypi.org/project/blacken-docs/
>
> I don't know if there is something similar possible in Java?
>
> As to the automated builds with Jekyll, there are likely some
> fixes made on https://github.com/biopython/biopython.github.io/
> which can be copied over.
>
> Peter
>
> On Mon, Jan 15, 2024 at 4:06 PM Gary Murphy <hilbertglm at gmail.com> wrote:
>> Thank you for getting back to me so quickly.  Yes, I am the Gary Murphy
>> that forked the source to take a look at it and understand how to build
>> it.  I should have posted the official github URL instead of my fork.
>>
>> I have some code that reads FASTA files using Java streams that I
>> haven't submitted a pull request for, but I wanted to have a handle on
>> how to document it if it was accepted.  Specifically,
>> _wiki/BioJava_CookBook_Core_FastaReadWrite.md is the one I updated
>> locally, but haven't pushed. I also noted a lot of formatting errors on
>> the source code in the Cookbook, so I would be changing those only when
>> I update a page... a global update would be pretty time-consuming.
>>
>> More generally, since I am learning the code base, I thought it would be
>> beneficial for me to add documentation when I learn how to do things in
>> the normal course of my job that I had to jump into the source code
>> and/or test cases to understand.
>>
>> The first thing I would be updating is how to update the documentation.
>> The Jekyll docker container is broken out of the gate, so I had to
>> figure out how to get the build server running locally to ensure my
>> changes were getting rendered properly.
>>
>> I have spent some time in the tutorials. They are extremely helpful and
>> seem to be more recently updated.
>>
>>
>> On 1/15/24 09:49, Peter Cock wrote:
>>> I'd guess the source you want is https://github.com/biojava/biojava.github.io
>>> but Gary Murphy's version https://github.com/hilbertglm/biojava.github.io.git
>>> looks to be the same right now - this is the main BioJava website and
>>> it does indeed look not to have been updated recently. This includes what
>>> used to be the wiki content (including the cookbook), now as markdown pages.
>>> This repository also includes API documentation.
>>>
>>> What specifically did you want to change here? e.g. An example URL
>>>
>>> See also https://github.com/biojava/biojava-tutorial which has been changed
>>> much more recently.
>>>
>>> Peter
>>>
>>> On Mon, Jan 15, 2024 at 2:53 PM Gary Murphy <hilbertglm at gmail.com> wrote:
>>>> 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.
>>>>
>>>> -----
>>>>
>>>> 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.
>>>>
>>>> I got the source for the Cookbook (https://github.com/hilbertglm/biojava.github.io.git), and it seems like it is a bit out of date with quite a few formatting issues for the source code.
>>>>
>>>> Before I start...
>>>>
>>>> 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
>>>> 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.
>>>>
>>>> Any thoughts would be appreciated.
>>>>
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