That is true, I can't believe I missed "f = open(f, 'w')", it was too obvious. Anyway, I changed the directory permission and now it was able to view the docs.
However, since I have windows and Ubuntu VM, working on Github desktop is not very convenient especially for permission issues with shared folders. What I did is I copied the downloaded/installed docs from my VM to windows and I was able to visualize them in my Github desktop repository, then created a branch and it seems to be working fine.
Now editing to my understanding, if we choose to continue with Github desktop, I could use an editor like Atom https://atom.io/ but if we choose Sphinx, there will be no need to work with Github desktop at all. is that right?
I would appreciate it if you can give me indication about how to make code changes.
In the meanwhile, this is what I was able to do with Atom.
1- I edited the "build\preview\tutorials\moving-pictures" just as an example
2- I added an external link to the word "google sheets" that takes you to it's website
Hey there @Ahmed_Abdelfattah - I didn’t forget about you. We are trying to get the 2018.6 release out the door, so it might take me another business day or two to respond - stay tuned!
@thermokarst don't worry about it and good luck with the new release!
I was actually able to go on with editing the docs and I think it's going well. Here are some of examples of what I did so far!
1- inline links
In this example I had to add a line "To learn more about demultiplexing of single-end and paired-end sequence reads and visualization of sequence quality information, see demux plugin." I did this only because there was no good place to add the link. If adding text is a problem I can avoid it.
3- was what you originally suggested and I thought it was elegant i.e. the link is embedded in the command.
Let me know what you think!
PS There something I noticed while working
are qiime tools available as a qiime plugin? or any where else except in Exporting and Importing data? other options such as extract, peek, inspect-metadata, and validate are not available in QIIME2 documentations. but maybe this is another topic for a different time!
But, I imagine there are many other headings where a link would make sense, so maybe we just play it by ear.
This looks great! Did you manually insert an <a href... tag in here? If so, this might not work as expected --- one of the ways QIIME 2 is tested is actually by running every single command block in the docs (that lets us ensure that anyone running the commands in the docs won't run into any issues). If we modify those commands (by inserting link markup), those test won't work anymore. You can check these test yourself by running make html in your dev env (warning, this can take at least an hour to run). This is the reason I suggested we revisit later, since it will require some edits to the existing test code. Let me know what you think!
These commands are called builtins, and are interface-specific. Ideally we would have better online q2cli docs to point users at, but, one step at a time I suppose!
Something we've kicked around forever is creating a generic description of a QIIME 2 action and then translating that to different UIs. I think that changes for that could include this idea really easily.
