[Biojava-l] Updating the Cookbook (Resend)

[Gary Murphy]

Okay. I will put efforts in that direction.  That will be easier.

On 1/16/24 13:01, Jose Duarte wrote:
> Just want to confirm that the preferred way to write documentation for 
> BioJava is through the tutorial github site that Peter points out: 
> https://github.com/biojava/biojava-tutorial
>
> The docs and tutorials in github.io <http://github.io> are quite 
> outdated and came from migrating the previous wiki. It really needs a 
> good clean up.
>
> Jose
>
>
> On Mon, 15 Jan 2024 at 08:39, Gary Murphy <hilbertglm at gmail.com> wrote:
>
>     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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