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  • Oct 23 16:08

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Joe Hamman
@jhamman
Seattle pangeans can expect a few boxes of donuts at alder hall c.9am. It will pay to be there in time 😉
Scott
@scollis
Is it just my imagination or is it taking longer than normal to spin up an server with an existing image.
Ryan Abernathey
@rabernat
Pangeo publication reporting form: https://forms.gle/yfCHEHU2LMZhtqgF8
Joe Hamman
@jhamman
@rsignell-usgs - are you around today?
epifanio
@epifanio
Hello @all I will attend Oceanhackweek in the next days.. since I am already in Seattle... I thought to join you at the Pangea meetings. Hope it is ok )
Ryan Abernathey
@rabernat
@phaustin :
def test_launch_binder(binder_url, repo, ref):
    build_url = binder_url + '/build/gh/{repo}/{ref}'.format(repo=repo, ref=ref)
    r = requests.get(build_url, stream=True)
    r.raise_for_status()
    for line in r.iter_lines():
        line = line.decode('utf8')
        if line.startswith('data:'):
            data = json.loads(line.split(':', 1)[1])
            if data.get('phase') == 'ready':
                notebook_url = data['url']
                token = data['token']
                break
    else:
        # This means we never got a 'Ready'!
        assert False

    headers = {
        'Authorization': 'token {}'.format(token)
    }
    r = requests.get(notebook_url + '/api', headers=headers)
    assert r.status_code == 200
    assert 'version' in r.json()

    r = requests.post(notebook_url + '/api/shutdown', headers=headers)
    assert r.status_code == 200

binder_url = 'https://binder.pangeo.io'
repo = 'pangeo-data/pangeo-ocean-examples'
ref = 'f73b92a'

test_launch_binder(binder_url, repo, ref)
Takes a few minutes
Lindsey Heagy
@lheagy
All, this was published yesterday on the growth of Syzygy, the Canadian deployments of JupyterHubs for researchers which @phaustin talked about yesterday, and the suggestion of a consortium that could serve universities and research groups who want to use interactive computing. Could be an interesting avenue for connection! https://blog.jupyter.org/national-scale-interactive-computing-2c104455e062
Kevin Paul
@kmpaul
Preliminary results of the STAC sprint from the Pangeo community meeting: https://docs.google.com/presentation/d/17MdoxIqw4hyfZC3L9UyyM8VG4Of-LBki9qZBHp8FWgU/edit?usp=sharing
Ryan Abernathey
@rabernat
Philip Austin
@phaustin
@rabernat -- is the markdown editor https://stackedit.io/ ?
Filipe
@ocefpaf

@rabernat this is a list of the new packages in conda-forge added during the sprints: https://github.com/conda-forge/staged-recipes/issues?utf8=%E2%9C%93&q=label%3Apangeo-sprint+

The list will be updated tomorrow with at list one more.

Sarah Bird
@birdsarah
@yuvipanda @ocefpaf if you're curious my un-upgradeable conda was because conda-meta/pinned had pinned conda to 4.5.* (conda/conda#6941)
Filipe
@ocefpaf
Geez. Glad you resolved it.
Ryan Abernathey
@rabernat

@rabernat -- is the markdown editor https://stackedit.io/ ?

No, it was https://manubot.org

I guess you have to do a little setup first (e.g. kubectl apply -f shared-nfs-staging.yaml --namespace nasa-staging)
Ryan Abernathey
@rabernat
Does anyone have an example of an intake catalog pointing at zarr datasets on S3?
Aimee Barciauskas
@abarciauskas-bgse
I was hoping to do this as a part of my sprint but didn't get to it :disappointed:
Joe Hamman
@jhamman
@andersy005 :arrow_heading_up:
Ryan Abernathey
@rabernat
For some reason, @tjcrone and I are have trouble making intake work with s3. I think Tim will open an intake issue.
Rob Fatland
@robfatland
Two questions: Who is going to the Princeton Workshop on Next Gen Cloud Research Infrastructure? My abstract is only tangentially about pangeo and I was thinking someone was going to attend to carry that banner but I'm not sure who that is. Second: Is gitter Lobby just any and all conversations?
Joe Hamman
@jhamman
Rob, @rabernat is subbmitting on cloud-native data formats (e.g. Zarr) and I am submitting on the Pangeo Cloud Architecture/Principles.
This gitter lobby is a place for general conversation but we tend to try to limit the depth of any conversation because its hard to track.
Anderson Banihirwe
@andersy005
@jhamman, @rabernat, I still haven't had time to create static intake catalog for the CESM1 LENS data in S3. What I have today is something that works with intake-esm: https://intake-esm.readthedocs.io/en/latest/notebooks/examples/cesm1-lens-aws.html
Rob Fatland
@robfatland
Ok first: Great. Second: The Princeton thing is Mon/Tues and I'm at the Cornell Cloud Forum the prior Wed/Thu/Fri so plan to kill the weekend wandering around Manhattan looking for sandbagger climbing gyms. And third: I'll keep my gitter discourse oh wait, cool ! PewDiePie > 1e8 subscribers!

plan to kill the weekend wandering around Manhattan looking for sandbagger climbing gyms

Would love to meet up when you're in the city

Scott
@scollis
Hey folks.. I am using the KubeCluster and want to write data back to the main binder machine for analysis in my workflow.. but the daksk workers get a permission denied error when trying to write back to the file system
Joe Hamman
@jhamman
Your workers don’t have access to the home directory of your notebook session.
Scott
@scollis
Thanks @jhamman .. is there a FS the workers can see?
Joe Hamman
@jhamman
No. Well, they all have their own persistent disk.
But if you want the data locally, you need to compute first.
Scott
@scollis
right, is there a way to copy back from the workers to the notebook session FS? I am generating grid data on the workers that would be too big to fit in memory if I bought it all back by a client.gather(future)
I guess I could push the data back in the futures and then loop over them and dispose of the data as I save..
Let me experiment with that.. fun :)
Pier
@PhenoloBoy
@scollis Hi, in which format are you going to save your data once back from the workers?
Scott
@scollis
netcdf.
I know.. I really need to learn XARR
Pier
@PhenoloBoy
can you process your data per lines?
Scott
@scollis
Its very nicely parallel.. a task per time step. So chunking by time is easy..
Pier
@PhenoloBoy
I've got to solve a similar problem and, in my case, the only solution has been an append results in a netCDF4 file
netcdf not xarray
Scott
@scollis
Cool. That’s the kind of thing I am looking at doing
Pier
@PhenoloBoy
you have to create an empty netCDF http://unidata.github.io/netcdf4-python/netCDF4/index.html and almost that's it
even if isn't a super clean method in my case has been the only solution
but be aware that netcdf has some problem over GC
so before you start with this approach have a look at some discussion about netCDF and the Cloud base infrastructures