Assessment of Ocean Colour temporal stability for ecological studies #13

chiaravol · 2024-03-16T07:21:12Z

Data Type

Satellite ECVs - Ocean

Assessment Category

Consistency Assessment

Dataset Name

satellite-ocean-colour

Question Number

1

Task ID

eqctier3-f3857f89-ee5f-460c-8fe4-47c3efac59aa

Zipped Notebook

ocean_color_timeseries.ipynb.zip

Environment

name: wp5
channels:
  - conda-forge
dependencies:
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  - setuptools=69.0.3=pyhd8ed1ab_0
  - shapely=2.0.2=py311h2032efe_1
  - shellingham=1.5.4=pyhd8ed1ab_0
  - simpervisor=1.0.0=pyhd8ed1ab_0
  - sip=6.7.12=py311hb755f60_0
  - six=1.16.0=pyh6c4a22f_0
  - snappy=1.1.10=h9fff704_0
  - sniffio=1.3.0=pyhd8ed1ab_0
  - snuggs=1.4.7=py_0
  - sortedcontainers=2.4.0=pyhd8ed1ab_0
  - soupsieve=2.5=pyhd8ed1ab_1
  - sparse=0.15.1=pyhd8ed1ab_1
  - sqlalchemy=2.0.27=py311h459d7ec_0
  - sqlite=3.45.1=h2c6b66d_0
  - stack_data=0.6.2=pyhd8ed1ab_0
  - statsmodels=0.14.1=py311h1f0f07a_0
  - structlog=24.1.0=pyhd8ed1ab_0
  - tblib=3.0.0=pyhd8ed1ab_0
  - tenacity=8.2.3=pyhd8ed1ab_0
  - terminado=0.18.0=pyh0d859eb_0
  - textwrap3=0.9.2=py_0
  - threadpoolctl=3.2.0=pyha21a80b_0
  - tiledb=2.19.1=h4386cac_0
  - tinycss2=1.2.1=pyhd8ed1ab_0
  - tk=8.6.13=noxft_h4845f30_101
  - toml=0.10.2=pyhd8ed1ab_0
  - tomli=2.0.1=pyhd8ed1ab_0
  - toolz=0.12.1=pyhd8ed1ab_0
  - tornado=6.3.3=py311h459d7ec_1
  - tqdm=4.66.2=pyhd8ed1ab_0
  - traitlets=5.14.1=pyhd8ed1ab_0
  - typer=0.9.0=pyhd8ed1ab_0
  - types-python-dateutil=2.8.19.20240106=pyhd8ed1ab_0
  - typing-extensions=4.9.0=hd8ed1ab_0
  - typing_extensions=4.9.0=pyha770c72_0
  - typing_utils=0.1.0=pyhd8ed1ab_0
  - tzcode=2024a=h3f72095_0
  - tzdata=2024a=h0c530f3_0
  - ucx=1.15.0=h75e419f_3
  - udunits2=2.2.28=h40f5838_3
  - uri-template=1.3.0=pyhd8ed1ab_0
  - uriparser=0.9.7=hcb278e6_1
  - urllib3=2.2.0=pyhd8ed1ab_0
  - wcwidth=0.2.13=pyhd8ed1ab_0
  - webcolors=1.13=pyhd8ed1ab_0
  - webencodings=0.5.1=pyhd8ed1ab_2
  - websocket-client=1.7.0=pyhd8ed1ab_0
  - wheel=0.42.0=pyhd8ed1ab_0
  - xarray=2024.1.1=pyhd8ed1ab_0
  - xarraymannkendall=1.4.5=pyhd8ed1ab_0
  - xcb-util=0.4.0=hd590300_1
  - xcb-util-image=0.4.0=h8ee46fc_1
  - xcb-util-keysyms=0.4.0=h8ee46fc_1
  - xcb-util-renderutil=0.3.9=hd590300_1
  - xcb-util-wm=0.4.1=h8ee46fc_1
  - xerces-c=3.2.5=hac6953d_0
  - xesmf=0.8.2=pyhd8ed1ab_0
  - xhistogram=0.3.2=pyhd8ed1ab_0
  - xkeyboard-config=2.41=hd590300_0
  - xorg-fixesproto=5.0=h7f98852_1002
  - xorg-inputproto=2.3.2=h7f98852_1002
  - xorg-kbproto=1.0.7=h7f98852_1002
  - xorg-libice=1.1.1=hd590300_0
  - xorg-libsm=1.2.4=h7391055_0
  - xorg-libx11=1.8.7=h8ee46fc_0
  - xorg-libxau=1.0.11=hd590300_0
  - xorg-libxdmcp=1.1.3=h7f98852_0
  - xorg-libxext=1.3.4=h0b41bf4_2
  - xorg-libxfixes=5.0.3=h7f98852_1004
  - xorg-libxi=1.7.10=h7f98852_0
  - xorg-libxrender=0.9.11=hd590300_0
  - xorg-renderproto=0.11.1=h7f98852_1002
  - xorg-xextproto=7.3.0=h0b41bf4_1003
  - xorg-xf86vidmodeproto=2.3.1=h7f98852_1002
  - xorg-xproto=7.0.31=h7f98852_1007
  - xskillscore=0.0.24=pyhd8ed1ab_0
  - xyzservices=2023.10.1=pyhd8ed1ab_0
  - xz=5.2.6=h166bdaf_0
  - yaml=0.2.5=h7f98852_2
  - yarl=1.9.4=py311h459d7ec_0
  - zarr=2.16.1=pyhd8ed1ab_0
  - zeromq=4.3.5=h59595ed_0
  - zict=3.0.0=pyhd8ed1ab_0
  - zipp=3.17.0=pyhd8ed1ab_0
  - zlib=1.2.13=hd590300_5
  - zstd=1.5.5=hfc55251_0
  - pip:
      - c3s-eqc-automatic-quality-control==0.1.2.dev103+gaf19fc1
      - cacholote==0.7.2
      - cads-toolbox==0.0.2b0
      - cgul==0.0.4
      - coucal==0.0.1b3
      - emohawk==0.0.4b0
      - kaleido==0.2.1
      - pymannkendall==1.4.3
prefix: /data/common/miniforge3/envs/wp5

Anything else we need to know?

No response

The text was updated successfully, but these errors were encountered:

malmans2 · 2024-03-18T08:00:52Z

Here is the permalink: https://github.com/ecmwf-projects/c3s2-eqc-quality-assessment/blob/2340920bbd0d169003f4015f456a0acf02467784/Satellite_ECVs/Ocean_ECVs/satellite_satellite-ocean-colour_consistency-assessment_q01.ipynb

Please make sure that the notebook name is correct.

If you need to make modifications, please share here the new version of the notebook and I will provide a new permalink.
Let me know when the notebook is accepted, I will merge the PR into main.

malmans2 · 2024-03-18T08:30:37Z

@chiaravol,

Did you delete your comment? Do you need a new permalink?

chiaravol · 2024-03-18T08:32:02Z

Hi Mattia,

I've just realized there was a small typo in the NB. Could you please provide a new permalink? Here the new zipped NB:

ocean_color_timeseries.ipynb.zip

Thanks

malmans2 · 2024-03-18T08:40:17Z

Here it is: https://github.com/ecmwf-projects/c3s2-eqc-quality-assessment/blob/c68aa33fa20352ee1b216184e7bd19303a2423d9/Satellite_ECVs/Ocean_ECVs/satellite_satellite-ocean-colour_consistency-assessment_q01.ipynb

(This is not the place to provide technical support, but I noticed you changed code in the cached functions. If you do that without invalidating the cache, the change does not affect the results. Are you aware of it? In case you need support, please open an issue here)

chiaravol · 2024-03-19T18:56:00Z

Hi Mattia. Thanks for the NB!
I re-run it and here the new zip file for the permalink:
ocean_color_timeseries.ipynb.zip

Cheers,
Chiara

malmans2 · 2024-03-20T08:40:18Z

Here it is: https://github.com/ecmwf-projects/c3s2-eqc-quality-assessment/blob/cb712777ccc7bac19715a7b3840c15455a771b23/Satellite_ECVs/Ocean_ECVs/satellite_satellite-ocean-colour_consistency-assessment_q01.ipynb

chiaravol · 2024-04-05T09:15:00Z

Hi Mattia, here the new NB:
ocean_color_timeseries.ipynb.zip

Thanks

malmans2 · 2024-04-05T09:55:56Z

Here is the new permalink: https://github.com/ecmwf-projects/c3s2-eqc-quality-assessment/blob/1fdb12b4cf91cc42da97fbf85bb8930c5cca652d/Satellite_ECVs/Ocean_ECVs/satellite_satellite-ocean-colour_consistency-assessment_q01.ipynb

chiaravol · 2024-04-05T15:10:36Z

Thanks Mattia

chiaravol · 2024-05-13T06:27:21Z

Hi Mattia, I need a new permalink for this notebook:

ocean_color_timeseries-Guided.ipynb.zip

Cheers

malmans2 · 2024-05-13T07:23:59Z

Here it is: https://github.com/ecmwf-projects/c3s2-eqc-quality-assessment/blob/ff59717e920988c324c7950aa738cd98b43a631a/Satellite_ECVs/Ocean_ECVs/satellite_satellite-ocean-colour_consistency-assessment_q01.ipynb

chiaravol · 2024-05-24T13:50:30Z

Hi Mattia, Could you please provide a new permalink
satellite_satellite-ocean-colour_consistency-assessment_q01.ipynb.zip

malmans2 · 2024-05-24T14:00:18Z

Here it is: https://github.com/ecmwf-projects/c3s2-eqc-quality-assessment/blob/78a281f815faa1dbeec5d681fb31c29a97bbd043/Satellite_ECVs/Ocean_ECVs/satellite_satellite-ocean-colour_consistency-assessment_q01.ipynb

chiaravol · 2024-06-10T14:37:38Z

Hi Mattia,
Could you please give me another permalink for the NB
satellite_satellite-ocean-colour_consistency-assessment_q01.ipynb.zip
Thanks

malmans2 · 2024-06-10T14:42:13Z

Here it is: https://github.com/ecmwf-projects/c3s2-eqc-quality-assessment/blob/b64b3ea2bf277e38dbc9ab321c10aa6488b5fb40/Satellite_ECVs/Ocean_ECVs/satellite_satellite-ocean-colour_consistency-assessment_q01.ipynb

chiaravol · 2024-07-09T10:21:54Z

Hi Mattia, I slightly modified the text in the NB and I need a new permalink for it.
satellite_satellite-ocean-colour_consistency-assessment_q01-Copy1.ipynb.zip

Cheers

malmans2 · 2024-07-09T10:44:06Z

Hi @chiaravol,

I added some check so we can catch formatting issues before we go to production.
You have a small issue in the last markdown:

WARNING: Non-consecutive header level increase; H2 to H4 [myst.header]

The fix is easy, Key resources and Reference should be one level below If you want to know more.
So either do this:

- ## If you want to know more
+ ### If you want to know more

#### References

#### References

Or this:

## If you want to know more

- #### Key resources
+ ### Key resources

- #### References
+ ### References

Hope it's clear! Could you please fix it and send me a new version?
Thanks!

chiaravol · 2024-07-09T11:17:54Z

There you go:
satellite_satellite-ocean-colour_consistency-assessment_q01-Copy1.ipynb.zip

Thanks for pointing this out.
Chiara

malmans2 · 2024-07-09T12:35:52Z

Here is the permalink: https://github.com/ecmwf-projects/c3s2-eqc-quality-assessment/blob/ea4b1fae960996e897b9e6348f8d70fdaee0040e/Satellite_ECVs/Ocean_ECVs/satellite_satellite-ocean-colour_consistency-assessment_q01.ipynb

chiaravol · 2024-07-10T06:18:04Z

Thanks Mattia!

malmans2 · 2024-10-22T15:57:53Z

Hi there,

I've aligned the notebook with the latest template. If you check the preview, you'll notice some minor formatting edits.
If you need to review this notebook, please make sure to start from the latest version.

Here is the latest permalink: https://github.com/ecmwf-projects/c3s2-eqc-quality-assessment/blob/cb8beb340ed9d74a8fe5e506eee69c30def30877/Satellite_ECVs/Ocean/satellite_satellite-ocean-colour_consistency-assessment_q01.ipynb

You don't need to re-submit the permalink; the last one you used is still valid.

chiaravol · 2024-10-24T10:57:08Z

Hi Mattia,
I slightly modified the text in the NB in the latest version due to new comments. Here the zip file:

satellite_satellite-ocean-colour_consistency-assessment_q01-Copy1.ipynb.zip

I also have a couple of issues that I cannot solve:

How can I deactivate the downloading bars?
I'm following the syntax, described in the NB template, to add links between Methodology and Analysis and results section, but it works only for the first two links and I cannot figure out why. Any ideas?
What's the syntax to collapse code cells?

Cheers,
Chiara

malmans2 · 2024-10-24T13:54:53Z

Hi @chiaravol,

I've made a couple of minor changes to align with the template (e.g., all sections in the template are mandatory).

How can I deactivate the downloading bars?

You need to re-run the notebook adding the argument quiet=True in download_and_transform.

I'm following the syntax, described in the NB template, to add links between Methodology and Analysis and results section, but it works only for the first two links and I cannot figure out why. Any ideas?

I think they are all working fine. The preview looks good to me.

What's the syntax to collapse code cells?

No need to worry about it. Our code takes care of it when we deploy the book.

This is the latest permalink: https://github.com/ecmwf-projects/c3s2-eqc-quality-assessment/blob/f7e3bd8f5134a746256414955f64fbb94824b368/Satellite_ECVs/Ocean/satellite_satellite-ocean-colour_consistency-assessment_q01.ipynb

If you need to make edits, please start from the notebook corresponding to the permalink above (e.g., click on the permalink, then download).

chiaravol · 2024-10-25T06:26:14Z

Hi Mattia,
Thank you very much for your work!
I run the NB again (using the last permalink you shared) to hide the downloading bars. Here, the zip file
satellite_satellite-ocean-colour_consistency-assessment_q01.ipynb.zip

malmans2 · 2024-10-25T06:43:17Z

OK, before I issue the new permalink, could you please send me the right Workflow ID?
It looks like this: eqctier3-1123e4567-e89b-12d3-a456-42665544000

chiaravol · 2024-10-25T06:47:58Z

I have no access to the task on CIM and I cannot check it out as I made a mistake yesterday and filled it instead of saving it :( So, I'm waiting for the task to be open again. I'll send you the workflow ID ASAP.

malmans2 · 2024-10-25T07:10:01Z

OK, no problem.

Here is the latest permalink: https://github.com/ecmwf-projects/c3s2-eqc-quality-assessment/blob/337b41a8b092d8cfc05d62dad5a1da9180453c38/Satellite_ECVs/Ocean/satellite_satellite-ocean-colour_consistency-assessment_q01.ipynb

chiaravol · 2024-10-28T08:27:33Z

Hi Mattia,

Here the Workflow ID you asked for: eqctier3-f3857f89-ee5f-460c-8fe4-47c3efac59aa

May I use the last permalink you shared now?

Cheers,
Chiara

malmans2 · 2024-10-28T09:11:22Z

If you haven't submitted the permalink yet, use this one which is associated with the correct ID: https://github.com/ecmwf-projects/c3s2-eqc-quality-assessment/blob/e8bcf34a5093485c3c6e208953ee65d59a337a80/Satellite_ECVs/Ocean/satellite_satellite-ocean-colour_consistency-assessment_q01.ipynb

PREVIEW

chiaravol · 2024-10-28T09:13:05Z

I didn't, so I am going to use this one.

Thanks :)

malmans2 mentioned this issue Mar 18, 2024

554f0b24-e154-11ee-8810-5279ad638b32 #16

Closed

malmans2 mentioned this issue Apr 5, 2024

Ocean Colour permalink #36

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malmans2 added the wp5 label May 16, 2024

chiaravol changed the title ~~Ocean Colour Time series~~ Assessment of Ocean Colour temporal stability for ecological studies May 24, 2024

malmans2 linked a pull request Oct 28, 2024 that will close this issue

eqctier3-f3857f89-ee5f-460c-8fe4-47c3efac59aa #247

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Assessment of Ocean Colour temporal stability for ecological studies #13

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Assessment of Ocean Colour temporal stability for ecological studies #13

Assessment of Ocean Colour temporal stability for ecological studies #13

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