Test all figures in preparation for updating production env to Python…

… 3.13 (#327)

* Add missing SPDX short-form license identifiers

Ensures compliance with licensing practices by adding SPDX license identifiers
to `make_plots.py` and `tracer_thalweg_and_surface_hourly.py`. This improves
clarity and streamlines license management across the codebase.

* Update tracer_thalweg_and_surface_hourly fig test notebook

Update test notebook for `tracer_thalweg_and_surface_hourly` figure module and
confirm that the module works in a production environment based on Python 3.13.

* Correct bathymetry file name in fig test notebook

Updated bathymetry file name in test notebook for
`tracer_thalweg_and_surface_hourly` figure module to `bathymetry_202108.nc`.

* Update velocity_section_and_surface fig test notebook

Update test notebook for `velocity_section_and_surface` figure module and
confirm that the module works in a production environment based on Python 3.13.

* Update README for research figures notebooks

Modernized `make_readme.py` script.

* Update broken links to CONTRIBUTORS in docs

Replaced outdated "master" branch links with "main" branch links in `README.rst`
and `docs/license_description.txt`. Ensures references to CONTRIBUTORS file are
accurate and functional.

* Add TestPlotVelNEGridded figure test notebook

Introduced a new notebook to test the `research_VENUS.plot_vel_NE_gridded()`
function. It replicates production settings for validation and highlights the
need for a refactor into a proper figure module. Updated README.md with the new
notebook entry and corrected a link typo.

* Update time_series_plots fig test notebook

Update test notebook for `time_series_plots` figure module and confirm that the
module works in a production environment based on Python 3.13.

* Update README for comparison figures notebooks

Modernized `make_readme.py` script.

* Update sandheads_winds fig test notebook

Update test notebook for `sandheads_winds` figure module and confirm that the
module works in a production environment based on Python 3.13.

* Update compare_venus_ctd fig test notebook

Update test notebook for `compare_venus_ctd` figure module and confirm that the
module works in a production environment based on Python 3.13.

* Change 'np.NaN' to 'np.nan' re: Numpy 2.0

'numpy.nan' is the correct spelling in Numpy 2.0. All others are deprecated.

Missed in PR #272.

* Update storm_surge_alerts_thumbnail fig test notebook

Update test notebook for `storm_surge_alerts_thumbnail` figure module and
confirm that the module works in a production environment based on Python 3.13.

* Update storm_surge_alerts fig test notebook

Update test notebook for `storm_surge_alerts` figure module and
confirm that the module works in a production environment based on Python 3.13.

* Update pt_atkinson_tide fig test notebook

Update test notebook for `pt_atkinson_tide` figure module and
confirm that the module works in a production environment based on Python 3.13.

* Adjust 10-min averaging to correctly offset timestamps

Removed the deprecated `loffset` parameter and manually adjusted the timestamps
with a calculated offset. Ensures proper alignment of resampled data timestamps
for accurate comparison.

* Re-run notebooks with Bitstream Vera fonts installed

This gets rid of the huge number of
`findfont: Font family 'Bitstream Vera Sans' not found` messages.

* Update compare_tide_prediction_max_ssh fig test notebook

Update test notebook for `compare_tide_prediction_max_ssh` figure module and
confirm that the module works in a production environment based on Python 3.13.

Halfmoon Bay dn Squamish figures commented out due to disappearance of obs from
CHS server.

* Update README for publish figures notebooks

Modernized `make_readme.py` script.

* Remove unnecessary column renaming in tide predictions

The column renaming for "pred_noshallow" in the ttide dataset is no longer
required thanks to SalishSeaCast/tools#132 and has
been removed. This improves code clarity and eliminates an unneeded operation.

* Update dict key for tidal prediction difference

Delete extra spaces in the "pred_noshallow" key that were eliminated at source
in SalishSeaCast/tools#132.

* Re-run notebooks after stormtools date parsing fix

This gets rid of a large number of FutureWarning messages.

* Update surface_current_tiles fig test notebook

Update test notebook for `surface_current_tiles` figure module and confirm that
the module works in a production environment based on Python 3.13.

* Update wave_height_period fig test notebook

Update test notebook for `wave_height_period` figure module and confirm that
the module works in a production environment based on Python 3.13.

* Update README for wwatch3 figures notebooks

Modernized `make_readme.py` script.

README.rst

@@ -87,7 +87,7 @@ License
 The SalishSeaCast ocean model automation system code and documentation are copyright 2013 – present
 by the `SalishSeaCast Project Contributors`_ and The University of British Columbia.
 
-.. _SalishSeaCast Project Contributors: https://github.com/SalishSeaCast/docs/blob/master/CONTRIBUTORS.rst
+.. _SalishSeaCast Project Contributors: https://github.com/SalishSeaCast/docs/blob/main/CONTRIBUTORS.rst
 
 They are licensed under the Apache License, Version 2.0.
 http://www.apache.org/licenses/LICENSE-2.0

docs/license_description.txt

@@ -8,4 +8,4 @@ They are licensed under the Apache License, Version 2.0.
 http://www.apache.org/licenses/LICENSE-2.0
 Please see the LICENSE file for details of the license.
 
-.. _SalishSeaCast Project Contributors: https://github.com/SalishSeaCast/docs/blob/master/CONTRIBUTORS.rst
+.. _SalishSeaCast Project Contributors: https://github.com/SalishSeaCast/docs/blob/main/CONTRIBUTORS.rst

notebooks/figures/comparison/README.md

@@ -3,10 +3,10 @@ the results figures generation modules of the SalishSeaCast automation system.
 
 The links below are to static renderings of the notebooks via
 [nbviewer.org](https://nbviewer.org/).
-Descriptions under the links below are from the first cell of the notebooks
+Descriptions below the links are from the first cell of the notebooks
 (if that cell contains Markdown or raw text).
 
-* ## [TestCompareVENUS_CTD.ipynb](https://nbviewer.org/github/SalishSeaCast/SalishSeaNowcast/blob/main/comparison/TestCompareVENUS_CTD.ipynb)
+* ## [TestCompareVENUS_CTD.ipynb](https://nbviewer.org/github/SalishSeaCast/SalishSeaNowcast/blob/main/notebooks/figures/comparison/TestCompareVENUS_CTD.ipynb)
 
     **Test `compare_venus_ctd` Module**
 
@@ -15,7 +15,7 @@ Descriptions under the links below are from the first cell of the notebooks
 
     Set-up and function call replicates as nearly as possible what is done in the `nowcast.workers.make_plots` worker.
 
-* ## [TestSalinityFerryTrackModule.ipynb](https://nbviewer.org/github/SalishSeaCast/SalishSeaNowcast/blob/main/comparison/TestSalinityFerryTrackModule.ipynb)
+* ## [TestSalinityFerryTrackModule.ipynb](https://nbviewer.org/github/SalishSeaCast/SalishSeaNowcast/blob/main/notebooks/figures/comparison/TestSalinityFerryTrackModule.ipynb)
 
     **Test `salinity_ferry_track` Module**
 
@@ -24,7 +24,7 @@ Descriptions under the links below are from the first cell of the notebooks
 
     Set-up and function call replicates as nearly as possible what is done in the `nowcast.workers.make_plots` worker.
 
-* ## [TestSandHeadsWinds.ipynb](https://nbviewer.org/github/SalishSeaCast/SalishSeaNowcast/blob/main/comparison/TestSandHeadsWinds.ipynb)
+* ## [TestSandHeadsWinds.ipynb](https://nbviewer.org/github/SalishSeaCast/SalishSeaNowcast/blob/main/notebooks/figures/comparison/TestSandHeadsWinds.ipynb)
 
     **Test `sandheads_winds` Module**
 
@@ -34,12 +34,12 @@ Descriptions under the links below are from the first cell of the notebooks
     to help ensure that the module will work in the nowcast production context.
 
 
-##License
+## License
 
-These notebooks and files are copyright 2013 – present
-by the SalishSeaCast Project Contributors
+These notebooks and files are copyright by the
+[SalishSeaCast Project Contributors](https://github.com/SalishSeaCast/docs/blob/main/CONTRIBUTORS.rst)
 and The University of British Columbia.
 
 They are licensed under the Apache License, Version 2.0.
-http://www.apache.org/licenses/LICENSE-2.0
-Please see the LICENSE file for details of the license.
+https://www.apache.org/licenses/LICENSE-2.0
+Please see the LICENSE file in this repository for details of the license.