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Merging #560 (818c0c5) into dev (219cad0) - See PR on Codacy

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Some nice additions, but also some new errors .. ;-)

Not a big fan of all the manual linking to rst files and notebooks. Why is this better? This is prone to errors, multiple links are already not working now because of this:

https://pastas--560.org.readthedocs.build/en/560/examples/index.html

A possible fix would be to implement nblink or some url checker. Also, there are new warnings given by ReadTheDocs that should be fixed first.

Not a big fan of all the manual linking to rst files and notebooks. Why is this better?

Now if you remove notebook 01_basic_model.ipynb from the examples folder with files:

00_prepare_timeseries.ipynb,
01_basic_model.ipynb,
02_fix_parameters.ipynb,
03_calibration_options.ipynb,
04_adding_rivers.ipynb,
05_adding_wells.ipynb,
06_multiple_wells.ipynb,
07_adding_trends.ipynb,
08_changing_responses.ipynb,
09_threshold_non_linear.ipynb,
10_non_linear_recharge.ipynb,
11_recharge_estimation.ipynb,
12_snowmodel.ipynb,
13_comparing_models.ipynb,
14_diagnostic_checking.ipynb,
15_timestep_analysis.ipynb,
16_uncertainty.ipynb,
17_emcee_uncertainty.ipynb,
18_sgi_example.ipynb,
19_signatures.ipynb

you have to rename:

00_prepare_timeseries.ipynb -> 00_prepare_timeseries.ipynb
02_fix_parameters.ipynb -> 01_fix_parameters.ipynb
03_calibration_options.ipynb -> 02_calibration_options.ipynb
04_adding_rivers.ipynb -> 03_adding_rivers.ipynb
05_adding_wells.ipynb -> 04_adding_wells.ipynb
06_multiple_wells.ipynb -> 05_multiple_wells.ipynb
07_adding_trends.ipynb -> 06_adding_trends.ipynb
08_changing_responses.ipynb -> 07_changing_responses.ipynb
09_threshold_non_linear.ipynb -> 08_threshold_non_linear.ipynb
10_non_linear_recharge.ipynb -> 09_non_linear_recharge.ipynb
11_recharge_estimation.ipynb -> 10_recharge_estimation.ipynb
12_snowmodel.ipynb -> 11_snowmodel.ipynb
13_comparing_models.ipynb -> 12_comparing_models.ipynb
14_diagnostic_checking.ipynb -> 13_diagnostic_checking.ipynb
15_timestep_analysis.ipynb -> 14_timestep_analysis.ipynb
16_uncertainty.ipynb -> 15_uncertainty.ipynb
17_emcee_uncertainty.ipynb -> 16_emcee_uncertainty.ipynb
18_sgi_example.ipynb -> 17_sgi_example.ipynb
19_signatures.ipynb -> 18_signatures.ipynb

With this change, you can simply adjust the index.rst file in the examples folder because al the files are listed there. Yes, you have to be tidy with the bookkeeping but that should not be too big of an issue.

Also, there are new warnings given by ReadTheDocs that should be fixed first.

Should all be good now.

Not a big fan of all the manual linking to rst files and notebooks. Why is this better?

Now if you remove notebook 01_basic_model.ipynb from the examples folder with files:

00_prepare_timeseries.ipynb,
01_basic_model.ipynb,
02_fix_parameters.ipynb,
03_calibration_options.ipynb,
04_adding_rivers.ipynb,
05_adding_wells.ipynb,
06_multiple_wells.ipynb,
07_adding_trends.ipynb,
08_changing_responses.ipynb,
09_threshold_non_linear.ipynb,
10_non_linear_recharge.ipynb,
11_recharge_estimation.ipynb,
12_snowmodel.ipynb,
13_comparing_models.ipynb,
14_diagnostic_checking.ipynb,
15_timestep_analysis.ipynb,
16_uncertainty.ipynb,
17_emcee_uncertainty.ipynb,
18_sgi_example.ipynb,
19_signatures.ipynb

you have to rename:

00_prepare_timeseries.ipynb -> 00_prepare_timeseries.ipynb
02_fix_parameters.ipynb -> 01_fix_parameters.ipynb
03_calibration_options.ipynb -> 02_calibration_options.ipynb
04_adding_rivers.ipynb -> 03_adding_rivers.ipynb
05_adding_wells.ipynb -> 04_adding_wells.ipynb
06_multiple_wells.ipynb -> 05_multiple_wells.ipynb
07_adding_trends.ipynb -> 06_adding_trends.ipynb
08_changing_responses.ipynb -> 07_changing_responses.ipynb
09_threshold_non_linear.ipynb -> 08_threshold_non_linear.ipynb
10_non_linear_recharge.ipynb -> 09_non_linear_recharge.ipynb
11_recharge_estimation.ipynb -> 10_recharge_estimation.ipynb
12_snowmodel.ipynb -> 11_snowmodel.ipynb
13_comparing_models.ipynb -> 12_comparing_models.ipynb
14_diagnostic_checking.ipynb -> 13_diagnostic_checking.ipynb
15_timestep_analysis.ipynb -> 14_timestep_analysis.ipynb
16_uncertainty.ipynb -> 15_uncertainty.ipynb
17_emcee_uncertainty.ipynb -> 16_emcee_uncertainty.ipynb
18_sgi_example.ipynb -> 17_sgi_example.ipynb
19_signatures.ipynb -> 18_signatures.ipynb

With this change, you can simply adjust the index.rst file in the examples folder because al the files are listed there. Yes, you have to be tidy with the bookkeeping but that should not be too big of an issue.

I hope you wrote a script to write that comment ;-) I can see your point.

checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/pastas/checkouts/560/doc/examples/diagnostic_checking.ipynb: WARNING: document isn't included in any toctree

Perhaps ReadTheDocs should throwing errors when these kind of things come up somehow. Now we have to manually check for errors in the built process to uncover this.

I hope you wrote a script to write that comment ;-) I can see your point.

👼 .
Also, not having to renaming the files constantly helps with the traceability of the git commit history.

Perhaps ReadTheDocs should throwing errors when these kind of things come up somehow. Now we have to manually check for errors in the built process to uncover this.

Agree

checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/pastas/checkouts/560/doc/examples/diagnostic_checking.ipynb: WARNING: document isn't included in any toctree

Fixed this, should be good now.

Nice work. Merging.