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The docs and tutorials in github.io are quite outdated and came from migrating the previous wiki.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 <hilbert...@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 <hilbert...@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 <hilbert...@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. > >>>> > >>>> _______________________________________________ > >>>> Biojava-l mailing list - Biojava-l@biojava.org > >>>> https://mailman.open-bio.org/mailman/listinfo/biojava-l > >>> _______________________________________________ > >>> Biojava-l mailing list - Biojava-l@biojava.org > >>> https://mailman.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > https://mailman.open-bio.org/mailman/listinfo/biojava-l >
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