Checking your install does not exist (returns 404)

[jankaWIS]

Hi Peer,

I'm coming to your workshop at Weizmann in 10 days. I was checking your instructions and just wanted to let you know that your page for checking installation doesn't exist.

curl -s https://raw.githubusercontent.com/PeerHerholz/workshop_weizmann/master/check_ins

returns 404.

[jankaWIS]

Speaking of 404, your link to opening an issue is wrong, you are missing an s at the end. https://github.com/PeerHerholz/workshop_weizmann/issues

Now it returns another 404..

[PeerHerholz]

Ahoi hoi @jankaWIS,

thx so much for spotting these problems! They should be fixed now. There might be a few more of these as I'm still preparing/finishing some sections of the workshop. Sorry for that.

Cheers, Peer

[jankaWIS]

One more thing regarding the same file (didn't want to open another issue), FYI on my machine, using:

conda install nibabel

results in

PackagesNotFoundError: The following packages are not available from current channels:

  - nibabel

The same goes for nilearn. Probably you want to recommend something like (source):

conda install -c conda-forge nilearn

or pip:

pip install -U --user nilearn

And one more note, nibabel is a dependency for nilearn so one can only install the latter.

[PeerHerholz]

Hi @jankaWIS,

thx for bringing this up. Would you mind sharing which installation instructions you follow? I'm asking because the setup section specifically mentions the command

conda config --append channels conda-forge

during the python section of the os-specific installation instructions.

[jankaWIS]

The once it gives you once you run the sh file we talked about before :), this: https://raw.githubusercontent.com/PeerHerholz/workshop_weizmann/master/check_install.sh

If you run it, it tells you how to install what is missing.

# check python packages
for package in ${packages[@]}; do
    python -c "import ${package}" 2> /dev/null || {
        package=$( echo "${package}" | tr '[:upper:]' '[:lower:]' )
        printf "Missing Python package:   "
        printf "install with $ conda install ${package}\n"
        missing=true
    }
done

[jankaWIS]

Ah, I see, you have there the command for conda to set it up as a default... I already had conda before so I skipped this part.

[PeerHerholz]

Hi @jankaWIS,

ah yes. I added a short primer for such cases in the setup instructions but it might be worth further specifying it.