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pierrepo / PBxplore

A suite of tools to explore protein structures with Protein Blocks :snake:
https://pbxplore.readthedocs.org/en/latest/
MIT License
28 stars 17 forks source link

[WIP] Rewrite of old documentation #110

Closed HubLot closed 8 years ago

HubLot commented 8 years ago

I rewrite the old documentation, written in Markdown, which was in the doc folder. Now, it's written with rest/sphinx and the files are in the doc-api. Hence, all documentation is in one place.

I described the installation and the utilization of the library. The utilization still needs enhancements for the API part. Then, from the previous markdown files, I described each utilization of the command-line tools.

This should solve issue #87 and #101.

What is still left to do:

Link to this PR's documentation: https://pbxplore-hub.readthedocs.org/en/doc/

HubLot commented 8 years ago

I set Read the Docs on my account so you can see the documentation of this PR. Here the link: https://pbxplore-hub.readthedocs.org/en/doc/

jbarnoud commented 8 years ago

Yeah! Looks great! I added a few inline comments. In addition it would be nice to have a bit more intro in the landing page to make the project more catchy.

jbarnoud commented 8 years ago

Also, it is not only the API doc anymore so the doc title should be changed on https://github.com/HubLot/PBxplore/blob/doc/doc-api/source/conf.py#L57. The doc-api directory could be renamed doc.

HubLot commented 8 years ago

Okay, I pushed few commits regarding our conversation and updated the PR description to reflect the updates.

jbarnoud commented 8 years ago

In the index page, 'PBxplore' got repeated in each subtitle (my bad). It may not be necessary. It could be nice, though, to have the pages about command line tools grouped under a subtitle (why not 'Command line interface'?).

HubLot commented 8 years ago

Yep, I know. I plan to remove those and regroup all cookbooks into one subtitle. But I need to modify the ipython notebooks. I prefer to let all the command lines tools in the menu (rather than grouped them under a subtitle) because I think it will be more clear for the user.

HubLot commented 8 years ago

Hi, I re-organize the index file of the documentation. I described a little more PBxplore, add authors, enhances the TOC.

Let me know what you think.

jbarnoud commented 8 years ago

I needed some time to get use to the change but it looks great !

pierrepo commented 8 years ago

I am not a big fan of rst doc but we don't have the choice here. I agree with the link to CC license. I guess MIT is fine by now for the code.

jbarnoud commented 8 years ago

Out of curiosity, what is it you do not like with rst doc?

On 12-01-16 17:29, Pierre Poulain wrote:

I am not a big fan of rst doc but we don't have the choice here. I agree with the link to CC license. I guess MIT is fine by now for the code.

— Reply to this email directly or view it on GitHub https://github.com/pierrepo/PBxplore/pull/110#issuecomment-170965588.

pierrepo commented 8 years ago

The way is handle links (to web sites and images) I guess ;-)

HubLot commented 8 years ago

I agree with the link to CC license.

Which one should I choose ? From my point of view, it seems the 4.0 is ok but I'm not an expert.

I guess MIT is fine by now for the code.

Okay, I'll add the licence.

pierrepo commented 8 years ago

For CC license: the lost recent one will fine.

HubLot commented 8 years ago

Okay, the last few commits:

There is still the issue #104 but I don't really know where to put the information and how to write it properly.

HubLot commented 8 years ago

At this point, if you are satisfied with my modifications, the PR can be merged. Documentation of clustering and Pypi availability can only be done once @jbarnoud 's PR is merged.

HubLot commented 8 years ago

@pierrepo is it good for you? Can you merge if so?