Adding papermill as a dependecy to the environment.yaml

[AndriiPovsten]

This papermill package is required to run AGC on REANA

Needed for iris-hep/analysis-grand-challenge#217

[oshadura]

@matthewfeickert would it be possible then to add new tag so we can use then new image at unpacked? Thanks!
Also are you considering the possibility of adding image as well to dockerhub?

[oshadura]

Actually we found that we can install dependencies via snakemake: https://snakemake.readthedocs.io/en/stable/tutorial/additional_features.html feel free to close PR if you don't find it useful.

[matthewfeickert]

@AndriiPovsten @oshadura sorry for the slow reply time — lots happening today.

Actually we found that we can install dependencies via snakemake: https://snakemake.readthedocs.io/en/stable/tutorial/additional_features.html feel free to close PR if you don't find it useful.

Okay, if you don't think you need anything here I'll close now. Though if you end up needing this just let me know and we can reopen it no problem. 👍

@AndriiPovsten I think you've explained this to me before, but can you remind me why papermill is needed, given that you can execute Jupyter notebooks from the command line with jupyter? Are you using papermill to hook into the notebooks to get particular values at different stages of the execution?

[AndriiPovsten]

Dear @matthewfeickert sorry for a late reply. Indeed normal Jupyter Notebook execution is possible via command line, I needed papermill in order to add parameters (which are a wildcards in our case) for each time the notebook is executing. Also it gives a sometimes useful statistics about time execution for a cell.
If something else (I think the servicex components) are required, I'll try to add them.

[matthewfeickert]

@AndriiPovsten The build is now failing as centos7 is now deprecated and so its mirrors seem to be deprecated as well.

# yum install -y bzip2                                               
Loaded plugins: fastestmirror, ovl
Loading mirror speeds from cached hostfile
Could not retrieve mirrorlist http://mirrorlist.centos.org/?release=7&arch=x86_64&repo=os&infra=container error was
14: curl#6 - "Could not resolve host: mirrorlist.centos.org; Unknown error"


 One of the configured repositories failed (Unknown),
 and yum doesn't have enough cached data to continue. At this point the only
 safe thing yum can do is fail. There are a few ways to work "fix" this:

     1. Contact the upstream for the repository and get them to fix the problem.

     2. Reconfigure the baseurl/etc. for the repository, to point to a working
        upstream. This is most often useful if you are using a newer
        distribution release than is supported by the repository (and the
        packages for the previous distribution release still work).

     3. Run the command with the repository temporarily disabled
            yum --disablerepo=<repoid> ...

     4. Disable the repository permanently, so yum won't use it by default. Yum
        will then just ignore the repository until you permanently enable it
        again or use --enablerepo for temporary usage:

            yum-config-manager --disable <repoid>
        or
            subscription-manager repos --disable=<repoid>

     5. Configure the failing repository to be skipped, if it is unavailable.
        Note that yum will try to contact the repo. when it runs most commands,
        so will have to try and fail each time (and thus. yum will be be much
        slower). If it is a very temporary problem though, this is often a nice
        compromise:

            yum-config-manager --save --setopt=<repoid>.skip_if_unavailable=true

Cannot find a valid baseurl for repo: base/7/x86_64

This might requires PR #30 to go in first.