repronim / howwouldrepronim

Sphinx for rendering the "How Would ReproNim Do That?" series of documents

HowWouldReproNim

Sphinx rendering of the "How Would ReproNim Do That?" series.

Building

Build the documentation:

# create a venv to not mess with anything else
virtualenv --python=python3.7 ~/env/repro
. ~/env/repro

# install from requirements.txt
pip install -r requirements.txt

# build the docs
make html

# view in browser
firefox _build/html/index.html

# build the PDF (this probably requires a lot of LaTeX stuff being installed,
# so no guarantee that it works out of the box ;-) 
make latexpdf

howwouldrepronim's Issues

Volume 9 conclusion

Volume 9 is missing the conclusion section.

Volume 9 unresolved references

From #15 :

Unresolved references:

• the last sentence of "In practice" (Windows users should consider using the Ubuntu subsystem (reference).)
• the third sentence of "Step 2" (Instead we are going to utilize virtualization techniques (reference?))
• also in "Step 2", the sentence "While it’s possible to build Windows containers (REFERENCE), macOS is not supported (not to say that maybe somewhere in northern California (no, not Napa Valley, a bit below) this exists)."

Import existing volumes

• Volume 1: How would ReproNim do a Local Container Analysis?
• Volume 2: How Would ReproNim Publish a Dataset?
• Volume 4: How Would ReproNim Manage Local FreeSurfer Results?
• Volume 6: How Would ReproNim Do an Analysis on ABCD Data?
  
• Volume 9: How Would ReproNim Containerize a Workflow?

Volume 9 missing appendix

From #15 :

Volume 9 is missing its appendix.

GitHub Stars (and link) point to DataLad

On the overview page: https://how-would.repronim.org/en/latest/index.html
in the left sidebar, under the ReproNim logo is a GitHub link and star counter display.

The link and star counter are for the DataLad handbook (https://github.com/datalad-handbook/book) which is nice, but probably not what we want. I presume that this should be the stars and link to https://github.com/ReproNim/HowWouldReproNim

I would have tried to fix this if I could have figures out where in hack that framing code lives...

This issue also exists in the left sidebbar of Volume 1 (and maybe other volumes, I've not checked yet).

Corrected concatenation

Hi all,

In step 5 the backslashes need to be removed, should be:

$ pynidm concat -nl "$(echo $(ls -1 */aseg_nidm.ttl) | tr " " "," )" -o allMTaseg.ttl

Volume 9 terminology

From #15 :

@PeerHerholz writes: "IIRC shape should be renamed to sulci as requested by the ENIGMA collaborators (@dnkennedy)?"

Volume 9 code formatting

From #15 :

@PeerHerholz writes: "there's same code here and there in the text and before I add those parts that are not rendered, we should talk about how we want to render it"

Publish to how-would.repronim.org