Added ROMS ocean model example notebook #3116

hetland · 2019-07-13T21:29:01Z

Fully documented, including whats-new.rst for all changes and api.rst for new API

This is an example of reading and visualizing ROMS model output. A highlight is adding a lazily calculated vertical coordinate. This notebook will need an example ROMS output file to run, called ROMS_example.nc. This will be uploaded to the data repository.

codecov · 2019-07-13T21:45:15Z

Codecov Report

Merging #3116 into scipy19-docs will increase coverage by <.01%.
The diff coverage is 100%.

@@               Coverage Diff                @@
##           scipy19-docs    #3116      +/-   ##
================================================
+ Coverage         95.99%   95.99%   +<.01%     
================================================
  Files                63       63              
  Lines             12796    12799       +3     
================================================
+ Hits              12284    12287       +3     
  Misses              512      512

* switching out examples to use nbsphinx * added jupyter_client to doc env * allow non netcdf tutorial files

rabernat · 2019-07-15T01:33:30Z

@hetland - thanks so much for this! Now that pydata/xarray-data#13 has been merged, can you try to update your example to use the xr.tutorial.open_dataset('ROMS_example.nc') function?

hetland · 2019-07-15T02:48:44Z

I'll try to get this done very soon.

…

On Sun, Jul 14, 2019 at 8:33 PM Ryan Abernathey ***@***.***> wrote: @hetland <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_hetland&d=DwMCaQ&c=u6LDEWzohnDQ01ySGnxMzg&r=T-gqCqhnaasy1XvN-p7wEw&m=iscthtGvDpXaFqvgH9LT53ecbC3ot7AaAZ-m0KOXKE8&s=hdRQyVYJ5Li194ZIzAWhJ0SsneZ15DdjqOya-Uegoo8&e=> - thanks so much for this! Now that pydata/xarray-data#13 <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_pydata_xarray-2Ddata_pull_13&d=DwMCaQ&c=u6LDEWzohnDQ01ySGnxMzg&r=T-gqCqhnaasy1XvN-p7wEw&m=iscthtGvDpXaFqvgH9LT53ecbC3ot7AaAZ-m0KOXKE8&s=8HH7PmBIx0_3Xe10MPEPiXoT0X_6Pj--82mnkmSXS8w&e=> has been merged, can you try to update your example to use the xr.tutorial.open_dataset('ROMS_example.nc') function? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_pydata_xarray_pull_3116-3Femail-5Fsource-3Dnotifications-26email-5Ftoken-3DAAT2YFXWQ23YSBUMI4YKYUDP7PHW7A5CNFSM4IDCS2Q2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZ4RU2Y-23issuecomment-2D511253099&d=DwMCaQ&c=u6LDEWzohnDQ01ySGnxMzg&r=T-gqCqhnaasy1XvN-p7wEw&m=iscthtGvDpXaFqvgH9LT53ecbC3ot7AaAZ-m0KOXKE8&s=ArFBmSuyA9yQqzaU4k0HRy5Ty4Fsn3lR8By69c4kjjs&e=>, or mute the thread <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AAT2YFUQZR7KG4FCGEAB2PDP7PHW7ANCNFSM4IDCS2QQ&d=DwMCaQ&c=u6LDEWzohnDQ01ySGnxMzg&r=T-gqCqhnaasy1XvN-p7wEw&m=iscthtGvDpXaFqvgH9LT53ecbC3ot7AaAZ-m0KOXKE8&s=SzNZLx3vqSjXyP508p1VXkBQ9WFnNIWR7JEjMTMHA0w&e=> .

-- Prof. Rob Hetland Texas A&M Univ. – Dept. of Oceanography http://pong.tamu.edu/~rob

added some extra documentation.

hetland · 2019-07-15T19:24:33Z

I'm having a hard time getting the docs to compile, they fail when loading the ROMS_example.nc file, though I switched to xr.tutorial.open_dataset('ROMS_example.nc'). Is there something else I need to do? I pushed a revised version.

rabernat · 2019-07-15T19:25:22Z

Can you post the error and stack trace?

rabernat · 2019-07-15T19:26:58Z

You have to rebase your feature branch on the upstream/scipy19-docs branch in order to get #3121 to work locally.

git fetch upstream
git rebase upstream/scipy19-docs

rabernat · 2019-07-15T19:33:14Z

I just saw the new PR (#3134). You don't need to start a new PR unless something is truly broken here. You can just keep pushing to this one.

added some extra documentation.

… scipy19-docs

hetland · 2019-07-16T18:43:34Z

OK, I closed the other pull request, and updated this branch.

dcherian · 2019-07-18T15:11:26Z

doc/examples/ROMS_ocean_model.ipynb

+    "import cartopy.feature as cfeature\n",
+    "import matplotlib.pyplot as plt\n",
+    "%matplotlib inline\n",
+    "# import cmocean   # TODO: Add this dependency to the docs\n",


Let's keep cmocean out since it isn't strictly necessary for the example.

dcherian · 2019-07-18T15:11:50Z

doc/examples/ROMS_ocean_model.ipynb

+    "ds = xr.tutorial.open_dataset('ROMS_example.nc', chunks={'ocean_time': 1})\n",
+    "\n",
+    "# This is a way to turn on chunking and lazy evaluation. Opening with mfdataset, or \n",
+    "# setting the chunking in the open_dataset would also achive this.\n",


Suggested change

"# setting the chunking in the open_dataset would also achive this.\n",

"# setting the chunking in the open_dataset would also achieve this.\n",

dcherian · 2019-07-18T15:13:46Z

doc/examples/ROMS_ocean_model.ipynb

+   "outputs": [],
+   "source": [
+    "section = ds.salt.isel(xi_rho=50, eta_rho=slice(0, 167), ocean_time=0)\n",
+    "section.plot(x='lon_rho', y='z_rho', figsize=(15, 6), cmap=cmocean.cm.haline, clim=(25, 35))\n",


Lets just use a standard matplotlib colormap

rabernat · 2019-08-02T10:24:50Z

I am returning to this after some vacation. Thanks so much @hetland for this great example!

The test failures are not related to this PR. I see only three things that need to be done to get this ready to merge.

Add a short introductory paragraph at the very top of the notebook with some very general backgroud. Remember we have users from tons of different fields (e.g. finance, bioinformatics); they will have no idea what ROMS stands for or even what an ocean model is. We need a few sentences to introduce this example and explain what it shows (primarily how to visualize data that has irregular / derived coordinate geometry)
Remove or resolve the commented-out code in the example.
Add credit to @hetland in whats-new.rst

… added citation in whats-new.

hetland · 2019-08-02T19:32:34Z

Hopefully these changes are all done now. I added my credit to 'Enhancements' instead of 'New functions/methods'; hope I guessed right. I didn't see any other examples of notebooks added.

…

On Fri, Aug 2, 2019 at 5:24 AM Ryan Abernathey ***@***.***> wrote: I am returning to this after some vacation. Thanks so much @hetland <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_hetland&d=DwMCaQ&c=u6LDEWzohnDQ01ySGnxMzg&r=T-gqCqhnaasy1XvN-p7wEw&m=6OwOv4lp3GGGKs1J1l2TyWR-fMyQK6bqwmVZSz5B_0A&s=9wZu4m94pOYewRGrzb8Hm4LFjT-B1u5RSGvnkDmWq5s&e=> for this great example! The test failures are not related to this PR. I see only three things that need to be done to get this ready to merge. - Add a short introductory paragraph at the very top of the notebook with some very general backgroud. Remember we have users from tons of different fields (e.g. finance, bioinformatics); they will have no idea what ROMS stands for or even what an ocean model is. We need a few sentences to introduce this example and explain what it shows (primarily how to visualize data that has irregular / derived coordinate geometry) - Remove or resolve the commented-out code in the example. - Add credit to @hetland <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_hetland&d=DwMCaQ&c=u6LDEWzohnDQ01ySGnxMzg&r=T-gqCqhnaasy1XvN-p7wEw&m=6OwOv4lp3GGGKs1J1l2TyWR-fMyQK6bqwmVZSz5B_0A&s=9wZu4m94pOYewRGrzb8Hm4LFjT-B1u5RSGvnkDmWq5s&e=> in whats-new.rst — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_pydata_xarray_pull_3116-3Femail-5Fsource-3Dnotifications-26email-5Ftoken-3DAAT2YFROYNHJ7S2DREKVOC3QCQDPRA5CNFSM4IDCS2Q2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3NLNPA-23issuecomment-2D517650108&d=DwMCaQ&c=u6LDEWzohnDQ01ySGnxMzg&r=T-gqCqhnaasy1XvN-p7wEw&m=6OwOv4lp3GGGKs1J1l2TyWR-fMyQK6bqwmVZSz5B_0A&s=t-z2yW4pb_z0ymnYO-k9w-VH5rMcQ050xTkIM9AKC5U&e=>, or mute the thread <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AAT2YFU4QP7IADADC2NTS3DQCQDPRANCNFSM4IDCS2QQ&d=DwMCaQ&c=u6LDEWzohnDQ01ySGnxMzg&r=T-gqCqhnaasy1XvN-p7wEw&m=6OwOv4lp3GGGKs1J1l2TyWR-fMyQK6bqwmVZSz5B_0A&s=8rqgwomPBkre8gH1dTw4pH2u67J2wpVX7h_2Eh80mCE&e=> .

-- Prof. Rob Hetland Texas A&M Univ. – Dept. of Oceanography http://pong.tamu.edu/~rob

rabernat · 2019-08-16T14:16:22Z

Thanks for this @hetland! I'm going to merge now!

rabernat · 2019-08-23T14:45:13Z

I finally got the page to build and it looks great!
http://xarray.pydata.org/en/scipy19-docs/examples/ROMS_ocean_model.html

There was an issue with the ROMS MD5 checksum which I fixed in pydata/xarray-data#17. The checksums .md5 files cannot have newlines at the end.

dcherian · 2019-08-23T16:11:06Z

It looks awesome!

hetland · 2019-08-23T16:18:04Z

I was wondering why the checksum kept failing. I'm glad that it's fixed now.

…

On Fri, Aug 23, 2019 at 9:11 AM Deepak Cherian ***@***.***> wrote: It looks awesome! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_pydata_xarray_pull_3116-3Femail-5Fsource-3Dnotifications-26email-5Ftoken-3DAAT2YFSAUGSDJVR3SMCFONTQGAD2BA5CNFSM4IDCS2Q2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5AU3WI-23issuecomment-2D524373465&d=DwMCaQ&c=u6LDEWzohnDQ01ySGnxMzg&r=T-gqCqhnaasy1XvN-p7wEw&m=jNHhw3-wczG-R1InYBWYHh1uySwOv2LvBhXHalRpLiM&s=4IE-mPoo-xIwygm2i5CE6JBKiZjK9AH9Acgx5swXjiM&e=>, or mute the thread <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AAT2YFQJTIUV6SXZI5H4EMLQGAD2BANCNFSM4IDCS2QQ&d=DwMCaQ&c=u6LDEWzohnDQ01ySGnxMzg&r=T-gqCqhnaasy1XvN-p7wEw&m=jNHhw3-wczG-R1InYBWYHh1uySwOv2LvBhXHalRpLiM&s=x5ZRvEPW7XBD1pfrzhF1Cszg_rgQ-qAyEysBTPrfTDY&e=> .

-- Prof. Rob Hetland Texas A&M Univ. – Dept. of Oceanography http://pong.tamu.edu/~rob

* change name of test env to xarray-tests (pydata#3110) * ROMS_ocean_model example added * Allow other tutorial filename extensions (pydata#3121) * switching out examples to use nbsphinx * added jupyter_client to doc env * allow non netcdf tutorial files * Changed load to xr.tutorial.open_dataset(), and added some extra documentation. * change name of test env to xarray-tests (pydata#3110) * ROMS_ocean_model example added * Changed load to xr.tutorial.open_dataset(), and added some extra documentation. * fixed colormap issues leftover from cmocean import * Added intro paragraph to ROMS example notebook, removed comments, and added citation in whats-new.

* Switch doc examples to use nbsphinx (#3105) * switching out examples to use nbsphinx * added jupyter_client to doc env * added ipykernel to doc env * Replace sphinx_gallery with notebook (#3106) * switching out examples to use nbsphinx * added jupyter_client to doc env * moved gallery to notebook * Allow other tutorial filename extensions (#3121) * switching out examples to use nbsphinx * added jupyter_client to doc env * allow non netcdf tutorial files * Added ROMS ocean model example notebook (#3116) * change name of test env to xarray-tests (#3110) * ROMS_ocean_model example added * Allow other tutorial filename extensions (#3121) * switching out examples to use nbsphinx * added jupyter_client to doc env * allow non netcdf tutorial files * Changed load to xr.tutorial.open_dataset(), and added some extra documentation. * change name of test env to xarray-tests (#3110) * ROMS_ocean_model example added * Changed load to xr.tutorial.open_dataset(), and added some extra documentation. * fixed colormap issues leftover from cmocean import * Added intro paragraph to ROMS example notebook, removed comments, and added citation in whats-new. * Add an example of ERA5 and GRIB data & visualization to the gallery (#3199) * Adds an example of ERA5 and GRIB data to the gallery * Add markdown narrative cells to GRIB example * Update load method to use xr.tutorial * Fix load method * require nbsphinx for the documentation builds * add more nbsphinx dependencies * install cfgrib using pip * add the eccodes library to the dependencies * remove the dependency on sphinx-gallery * add the ERA5 GRIB example to the list * update the documentation links Missing: section links in visualization_gallery.ipynb don't work yet, also the one in io.rst (it has a unicode char). * Fix leap year condition in monthly means example (#3464) * Typo correction in docs (#3387) * Update terminology.rst (#3455) Fixed broken link * Error in leap year? I've tried this script; however, it adds +1 to all months of the leap years. It sounds like an error, or I am wrong? So I wrote the condition "and month == 2" line 86 so that only the month of February gets +1. * Fix leap year (#3464) * Update doc/whats-new.rst Co-Authored-By: Deepak Cherian <[email protected]> * fix the reference to the rasterio geocoordinates docs * update whats-new.rst

zdgriffith and others added 2 commits July 13, 2019 14:21

change name of test env to xarray-tests (#3110)

4963110

ROMS_ocean_model example added

7630d6d

Allow other tutorial filename extensions (#3121)

5df8a42

* switching out examples to use nbsphinx * added jupyter_client to doc env * allow non netcdf tutorial files

Changed load to xr.tutorial.open_dataset(), and

9254769

added some extra documentation.

zdgriffith and others added 4 commits July 16, 2019 10:56

change name of test env to xarray-tests (#3110)

057f100

ROMS_ocean_model example added

41ee209

Changed load to xr.tutorial.open_dataset(), and

e2960dd

added some extra documentation.

Merge branch 'scipy19-docs' of https://github.com/hetland/xarray into…

d376137

… scipy19-docs

dcherian reviewed Jul 18, 2019

View reviewed changes

fixed colormap issues leftover from cmocean import

cec0241

Added intro paragraph to ROMS example notebook, removed comments, and…

37cbae7

… added citation in whats-new.

rabernat merged commit 79aa804 into pydata:scipy19-docs Aug 16, 2019

keewis mentioned this pull request Nov 21, 2019

merge scipy19 docs #3557

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Added ROMS ocean model example notebook #3116

Added ROMS ocean model example notebook #3116

hetland commented Jul 13, 2019 •

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	"# setting the chunking in the open_dataset would also achive this.\n",
	"# setting the chunking in the open_dataset would also achieve this.\n",

Added ROMS ocean model example notebook #3116

Added ROMS ocean model example notebook #3116

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