Update notebooks to 0.6.3, index/front page, and README

emiliom commented 1 year ago

Update the 3 notebooks to run with 0.6.3. Includes:

Replace explicit code with ep.consolidate.swap_dims_channel_frequency, introduced after 0.6.0
In each notebook, fix link to conda environment.yml file
Small polish to text such as typos; and for the OOI notebook, removed a stray sentence that shouldn't have been there
Replace the index (front page) notebook with a markdown file, index.md. That's much easier to maintain and update.

Updated the front page with information about creating the conda environment and running it in binder (I copied and tweaked the binder info from the README); and added information to the README file about building the JupytertBook locally.

Note: In the hake notebook, I removed cell 2 after running the notebook, so the cell numbering now skips from cell 1 to cell 3. I had added an ep.verbose statement in cell 2, but I later realized that it was unnecessary b/c the behavior I was specifying was already the default.

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emiliom commented 1 year ago

@leewujung How about we edit the title of the OOI notebook so it specifically says "OOI"? eg: "Watching a solar eclipse using an OOI moored echosounder". The hake notebook explicit mentions the hake survey in its title. I think OOI folks would appreciate the greater explicitness and visibility.

leewujung commented 1 year ago

Yes!

emiliom commented 1 year ago

How about we edit the title of the OOI notebook so it specifically says "OOI"? eg: "Watching a solar eclipse using an OOI moored echosounder"

Done

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leewujung commented on 2022-11-04T17:32:10Z ----------------------------------------------------------------

Assemble a list of EchoData object from the converted Zarr files.

How about changing this to:

Assemble a list of EchoData object from the converted Zarr files and combine them into a single EchoData object using the combine_echodata function.

And of course the following sentence needs to be tweaked a bit.

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leewujung commented on 2022-11-04T17:32:11Z ----------------------------------------------------------------

Suggest changes to make it explicitly that it is the combined object:

The Provenance group of the combined EchoData object now contains some helpful information compiled from the source files.

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leewujung commented on 2022-11-04T17:34:57Z ----------------------------------------------------------------

Note that this step is possible only because there are no duplicated frequencies present.

Small change:

Note that this step is possible only when there are no duplicated frequencies present.

leewujung commented 1 year ago

Ok, thanks @emiliom , I've finally reviewed this. Everything looks good and I made some minor suggested changes. I think the main README to benefit from adding some subheadings, but in the spirit to getting this updated first, feel free to merge after those changes are done. I'll do a separate PR on the subheadings.

emiliom commented 1 year ago

Thanks for the review. I've pushed the changes you suggested; BTW, wouldn't it be nice if GitHub + ReviewNB allowed for direct suggestions to be made for notebook markdown cells, and for direct merging?!

Feel free to submit a PR for the README file any time :stuck_out_tongue_winking_eye:

Merging. Woo-hoo!

OSOceanAcoustics / echopype-examples

Update notebooks to 0.6.3, index/front page, and README #27