MHKiT-Python v0.7.0

[akeeste]

• [x] add new content for v0.7
• [x] build new html for v0.7 content
• [x] confirm changes are building correctly

[akeeste]

When compiling the new docs for v0.7, I'm getting many repeated error and warning messages about minor formatting items. It doesn't seem like these issues typically prevent the docs from building completely, but it is difficult to identify problems with so many errors. I'll work through these as possible, but I think this issue points to a larger need for:

• automatic documentation builds
• test for documentation building, especially as most content is coming from function APIs in the other MHKiT repos

Error/warning log below. I'll update this thread with my progress. I'm using the most up to date MHKiT environment allowed with Python 3.9

[akeeste]

(mhkit_docs) C:\Users\akeeste\Documents\Software\GitHub\MHKiT\docs>make html
..\MHKiT-Python\examples\ADCP_Delft3D_TRTS_example.ipynb
..\MHKiT-Python\examples\adcp_example.ipynb
..\MHKiT-Python\examples\adv_example.ipynb
..\MHKiT-Python\examples\cdip_example.ipynb
..\MHKiT-Python\examples\Delft3D_example.ipynb
..\MHKiT-Python\examples\directional_waves.ipynb
..\MHKiT-Python\examples\environmental_contours_example.ipynb
..\MHKiT-Python\examples\extreme_response_contour_example.ipynb
..\MHKiT-Python\examples\extreme_response_full_sea_state_example.ipynb
..\MHKiT-Python\examples\extreme_response_MLER_example.ipynb
..\MHKiT-Python\examples\loads_example.ipynb
..\MHKiT-Python\examples\metocean_example.ipynb
..\MHKiT-Python\examples\mooring_example.ipynb
..\MHKiT-Python\examples\PacWave_resource_characterization_example.ipynb
..\MHKiT-Python\examples\power_example.ipynb
..\MHKiT-Python\examples\qc_example.ipynb
..\MHKiT-Python\examples\river_example.ipynb
..\MHKiT-Python\examples\short_term_extremes_example.ipynb
..\MHKiT-Python\examples\SWAN_example.ipynb
..\MHKiT-Python\examples\tidal_example.ipynb
..\MHKiT-Python\examples\tidal_performance_example.ipynb
..\MHKiT-Python\examples\wave_example.ipynb
..\MHKiT-Python\examples\wecsim_example.ipynb
..\MHKiT-Python\examples\WPTO_hindcast_example.ipynb
       24 file(s) copied.
Running Sphinx v6.2.1
WARNING: html_static_path entry '_static' is placed inside outdir
checking bibtex cache... out of date
parsing bibtex file C:\Users\akeeste\Documents\Software\GitHub\MHKiT\docs\source\MHKiT-Python.bib... parsed 1 entries
parsing bibtex file C:\Users\akeeste\Documents\Software\GitHub\MHKiT\docs\source\MHKiT-MATLAB.bib... parsed 1 entries
[autosummary] generating autosummary for: ADCP_Delft3D_TRTS_example.ipynb, Delft3D_example.ipynb, PacWave_resource_characterization_example.ipynb, SWAN_example.ipynb, WPTO_hindcast_example.ipynb, adcp_example.ipynb, adv_example.ipynb, cdip_example.ipynb, citeus.rst, contact.rst, ..., terminology.rst, tidal.rst, tidal_example.ipynb, tidal_performance_example.ipynb, troubleshooting.rst, utils.rst, wave.rst, wave_example.ipynb, webinars.rst, wecsim_example.ipynb
WARNING: [sphinxcontrib-matlabdomain] Unexpected class attribute: 'TestTags'.  In 'mhkit.tests.Loads_TestLoads'.
building [mo]: targets for 0 po files that are out of date
writing output...
building [html]: targets for 61 source files that are out of date
updating environment: [new config] 61 added, 0 changed, 0 removed
reading sources... [100%] wecsim_example
C:\Users\akeeste\Documents\Software\GitHub\MHKiT\docs\source\ADCP_Delft3D_TRTS_example.ipynb:63: WARNING: image file not readable: data/river/ADCP_transect/TRTS_transect_map.png
C:\Users\akeeste\Documents\Software\GitHub\MHKiT\docs\source\ADCP_Delft3D_TRTS_example.ipynb:63: WARNING: image file not readable: data/river/ADCP_transect/TRTS_transect_map.png
C:\Users\akeeste\Documents\Software\GitHub\MHKiT\docs\source\SWAN_example.ipynb:11: WARNING: Inline emphasis start-string without end-string.
C:\Users\akeeste\Documents\Software\GitHub\MHKiT\docs\source\SWAN_example.ipynb:41: WARNING: Inline emphasis start-string without end-string.
docstring of mhkit.qc.check_delta:30: WARNING: Definition list ends without a blank line; unexpected unindent.
WARNING: [sphinxcontrib-matlabdomain] Failed to import module 'mhkit.river.io'; the following exception was raised:
Traceback (most recent call last):
  File "C:\Users\akeeste\anaconda3\envs\mhkit_docs\lib\site-packages\sphinxcontrib\mat_documenters.py", line 140, in import_object
    self.object = entities_table[lookup_name]
KeyError: 'mhkit.river.io'

docstring of mhkit.tidal.io.request_noaa_data:17: ERROR: Unexpected indentation.
docstring of mhkit.tidal.io.request_noaa_data:18: WARNING: Block quote ends without a blank line; unexpected unindent.
docstring of mhkit.utils.magnitude_phase:7: WARNING: Definition list ends without a blank line; unexpected unindent.
docstring of mhkit.utils.magnitude_phase:14: ERROR: Unexpected indentation.
docstring of mhkit.wave.IO.hindcast.request_wpto:13: ERROR: Unexpected indentation.
docstring of mhkit.wave.IO.hindcast.request_wpto:15: WARNING: Block quote ends without a blank line; unexpected unindent.
docstring of mhkit.wave.IO.hindcast.request_wpto:28: CRITICAL: Unexpected section title.

Returns
-------
docstring of mhkit.wave.IO.NDBC.NDBC_available_data:14: ERROR: Unexpected indentation.
docstring of mhkit.wave.IO.NDBC.NDBC_available_data:15: WARNING: Block quote ends without a blank line; unexpected unindent.
docstring of mhkit.wave.IO.NDBC.NDBC_request_data:17: ERROR: Unexpected indentation.
docstring of mhkit.wave.IO.NDBC.NDBC_request_data:18: WARNING: Block quote ends without a blank line; unexpected unindent.
docstring of mhkit.wave.graphics.plot_chakrabarti:22: CRITICAL: Unexpected section title or transition.

--------
c:\users\akeeste\documents\software\github\mhkit\mhkit-python\mhkit\dolfyn\rotate\api.py:docstring of mhkit.dolfyn.rotate.api.calc_principal_heading:16: ERROR: Unexpected indentation.
C:\Users\akeeste\Documents\Software\GitHub\MHKiT\docs\source\mhkit-python\api.dolfyn.rst:225: WARNING: autosummary: failed to import mhkit.dolfyn.binned.VelBinner.bin_average.
Possible hints:
* ModuleNotFoundError: No module named 'mhkit.dolfyn.adv.motion.correct_motion'; 'mhkit.dolfyn.adv.motion' is not a package
* ModuleNotFoundError: No module named 'mhkit.dolfyn.binned.VelBinner'; 'mhkit.dolfyn.binned' is not a package
* AttributeError: 'function' object has no attribute 'mhkit'
* AttributeError: module 'mhkit.dolfyn.binned' has no attribute 'VelBinner'
C:\Users\akeeste\Documents\Software\GitHub\MHKiT\docs\source\mhkit-python\api.dolfyn.rst:225: WARNING: autosummary: failed to import mhkit.dolfyn.binned.VelBinner.bin_variance.
Possible hints:
* ModuleNotFoundError: No module named 'mhkit.dolfyn.adv.motion.correct_motion'; 'mhkit.dolfyn.adv.motion' is not a package
* ModuleNotFoundError: No module named 'mhkit.dolfyn.binned.VelBinner'; 'mhkit.dolfyn.binned' is not a package
* AttributeError: 'function' object has no attribute 'mhkit'
* AttributeError: module 'mhkit.dolfyn.binned' has no attribute 'VelBinner'
C:\Users\akeeste\Documents\Software\GitHub\MHKiT\docs\source\mhkit-python\api.dolfyn.rst:225: WARNING: autosummary: failed to import mhkit.dolfyn.binned.VelBinner.autocovariance.
Possible hints:
* ModuleNotFoundError: No module named 'mhkit.dolfyn.adv.motion.correct_motion'; 'mhkit.dolfyn.adv.motion' is not a package
* ModuleNotFoundError: No module named 'mhkit.dolfyn.binned.VelBinner'; 'mhkit.dolfyn.binned' is not a package
* AttributeError: 'function' object has no attribute 'mhkit'
* AttributeError: module 'mhkit.dolfyn.binned' has no attribute 'VelBinner'
c:\users\akeeste\documents\software\github\mhkit\mhkit-python\mhkit\dolfyn\velocity.py:docstring of mhkit.dolfyn.velocity.Velocity.set_declination:18: WARNING: Bullet list ends without a blank line; unexpected unindent.
c:\users\akeeste\documents\software\github\mhkit\mhkit-python\mhkit\dolfyn\velocity.py:docstring of mhkit.dolfyn.velocity.Velocity.set_declination:22: WARNING: Bullet list ends without a blank line; unexpected unindent.
c:\users\akeeste\documents\software\github\mhkit\mhkit-python\mhkit\dolfyn\velocity.py:docstring of mhkit.dolfyn.velocity.Velocity.set_declination:27: WARNING: Bullet list ends without a blank line; unexpected unindent.
c:\users\akeeste\documents\software\github\mhkit\mhkit-python\mhkit\dolfyn\velocity.py:docstring of mhkit.dolfyn.velocity.Velocity.set_declination:30: WARNING: Bullet list ends without a blank line; unexpected unindent.
c:\users\akeeste\documents\software\github\mhkit\mhkit-python\mhkit\dolfyn\velocity.py:docstring of mhkit.dolfyn.velocity.Velocity.set_declination:33: WARNING: Bullet list ends without a blank line; unexpected unindent.
C:\Users\akeeste\Documents\Software\GitHub\MHKiT\docs\source\mhkit-python\api.dolfyn.rst:257: WARNING: autosummary: failed to import mhkit.dolfyn.adv.turbulence.reynolds_stress.
Possible hints:
* ModuleNotFoundError: No module named 'mhkit.dolfyn.adv.turbulence.reynolds_stress'; 'mhkit.dolfyn.adv.turbulence' is not a package
* AttributeError: module 'mhkit.dolfyn.adv.turbulence' has no attribute 'reynolds_stress'
* ImportError:
* ModuleNotFoundError: No module named 'mhkit.dolfyn.velocity.mhkit'; 'mhkit.dolfyn.velocity' is not a package
* AttributeError: module 'mhkit.dolfyn.velocity' has no attribute 'mhkit'
C:\Users\akeeste\Documents\Software\GitHub\MHKiT\docs\source\mhkit-python\api.dolfyn.rst:257: WARNING: autosummary: failed to import mhkit.dolfyn.adv.turbulence.cross_spectral_density.
Possible hints:
* AttributeError: module 'mhkit.dolfyn.adv.turbulence' has no attribute 'cross_spectral_density'
* ImportError:
* ModuleNotFoundError: No module named 'mhkit.dolfyn.velocity.mhkit'; 'mhkit.dolfyn.velocity' is not a package
* ModuleNotFoundError: No module named 'mhkit.dolfyn.adv.turbulence.cross_spectral_density'; 'mhkit.dolfyn.adv.turbulence' is not a package
* AttributeError: module 'mhkit.dolfyn.velocity' has no attribute 'mhkit'
c:\users\akeeste\documents\software\github\mhkit\mhkit-python\mhkit\dolfyn\adv\turbulence.py:docstring of mhkit.dolfyn.adv.turbulence.ADVBinner.dissipation_rate_LT83:20: WARNING: Inline interpreted text or phrase reference start-string without end-string.
c:\users\akeeste\documents\software\github\mhkit\mhkit-python\mhkit\dolfyn\time.py:docstring of mhkit.dolfyn.time.epoch2date:15: ERROR: Undefined substitution referenced: "dlfn".
c:\users\akeeste\documents\software\github\mhkit\mhkit-python\mhkit\dolfyn\time.py:docstring of mhkit.dolfyn.time.epoch2date:15: ERROR: Undefined substitution referenced: "dlfn".
C:\Users\akeeste\Documents\Software\GitHub\MHKiT\docs\source\mhkit-python\api.mooring.rst:32: WARNING: autosummary: failed to import mhkit.mooring.main.read_moordyn.
Possible hints:
* ImportError:
* ModuleNotFoundError: No module named 'mhkit.mooring.main.read_moordyn'; 'mhkit.mooring.main' is not a package
* AttributeError: module 'mhkit.mooring.io' has no attribute 'mhkit'
* AttributeError: module 'mhkit.mooring.main' has no attribute 'read_moordyn'
* ModuleNotFoundError: No module named 'mhkit.mooring.io.mhkit'; 'mhkit.mooring.io' is not a package
c:\users\akeeste\documents\software\github\mhkit\mhkit-python\mhkit\river\io\d3d.py:docstring of mhkit.river.io.d3d.create_points:26: WARNING: Block quote ends without a blank line; unexpected unindent.
c:\users\akeeste\documents\software\github\mhkit\mhkit-python\mhkit\river\io\d3d.py:docstring of mhkit.river.io.d3d.turbulent_intensity:25: ERROR: Unexpected indentation.
c:\users\akeeste\documents\software\github\mhkit\mhkit-python\mhkit\river\io\d3d.py:docstring of mhkit.river.io.d3d.turbulent_intensity:29: ERROR: Unexpected indentation.
c:\users\akeeste\documents\software\github\mhkit\mhkit-python\mhkit\river\io\d3d.py:docstring of mhkit.river.io.d3d.turbulent_intensity:30: WARNING: Block quote ends without a blank line; unexpected unindent.
c:\users\akeeste\documents\software\github\mhkit\mhkit-python\mhkit\tidal\performance.py:docstring of mhkit.tidal.performance.power_curve:1: WARNING: duplicate object description of mhkit.tidal.performance.power_curve, other instance in mhkit-python/api.tidal, use :noindex: for one of them
c:\users\akeeste\documents\software\github\mhkit\mhkit-python\mhkit\tidal\performance.py:docstring of mhkit.tidal.performance.device_efficiency:1: WARNING: duplicate object description of mhkit.tidal.performance.device_efficiency, other instance in mhkit-python/api.tidal, use :noindex: for one of them
c:\users\akeeste\documents\software\github\mhkit\mhkit-python\mhkit\wave\io\hindcast\hindcast.py:docstring of mhkit.wave.io.hindcast.hindcast.request_wpto_point_data:16: ERROR: Unexpected indentation.
c:\users\akeeste\documents\software\github\mhkit\mhkit-python\mhkit\wave\io\hindcast\hindcast.py:docstring of mhkit.wave.io.hindcast.hindcast.request_wpto_point_data:20: WARNING: Block quote ends without a blank line; unexpected unindent.
c:\users\akeeste\documents\software\github\mhkit\mhkit-python\mhkit\wave\io\hindcast\wind_toolkit.py:docstring of mhkit.wave.io.hindcast.wind_toolkit.request_wtk_point_data:19: ERROR: Unexpected indentation.
C:\Users\akeeste\Documents\Software\GitHub\MHKiT\docs\source\webinars.rst:19: WARNING: Explicit markup ends without a blank line; unexpected unindent.
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [100%] wecsim_example
C:\Users\akeeste\Documents\Software\GitHub\MHKiT\docs\source\ADCP_Delft3D_TRTS_example.ipynb:: WARNING: Pygments lexer name 'ipython3' is not known
C:\Users\akeeste\Documents\Software\GitHub\MHKiT\docs\source\ADCP_Delft3D_TRTS_example.ipynb:: WARNING: Pygments lexer name 'ipython3' is not known
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C:\Users\akeeste\Documents\Software\GitHub\MHKiT\docs\source\ADCP_Delft3D_TRTS_example.ipynb:: WARNING: Pygments lexer name 'ipython3' is not known
C:\Users\akeeste\Documents\Software\GitHub\MHKiT\docs\source\ADCP_Delft3D_TRTS_example.ipynb:: WARNING: Pygments lexer name 'ipython3' is not known
C:\Users\akeeste\Documents\Software\GitHub\MHKiT\docs\source\ADCP_Delft3D_TRTS_example.ipynb:: WARNING: Pygments lexer name 'ipython3' is not known
C:\Users\akeeste\Documents\Software\GitHub\MHKiT\docs\source\ADCP_Delft3D_TRTS_example.ipynb:: WARNING: Pygments lexer name 'ipython3' is not known
C:\Users\akeeste\Documents\Software\GitHub\MHKiT\docs\source\ADCP_Delft3D_TRTS_example.ipynb:: WARNING: Pygments lexer name 'ipython3' is not known
C:\Users\akeeste\Documents\Software\GitHub\MHKiT\docs\source\ADCP_Delft3D_TRTS_example.ipynb:: WARNING: Pygments lexer name 'ipython3' is not known
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C:\Users\akeeste\Documents\Software\GitHub\MHKiT\docs\source\ADCP_Delft3D_TRTS_example.ipynb:: WARNING: Pygments lexer name 'ipython3' is not known
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C:\Users\akeeste\Documents\Software\GitHub\MHKiT\docs\source\ADCP_Delft3D_TRTS_example.ipynb:: WARNING: Pygments lexer name 'ipython3' is not known
C:\Users\akeeste\Documents\Software\GitHub\MHKiT\docs\source\ADCP_Delft3D_TRTS_example.ipynb:: WARNING: Pygments lexer name 'ipython3' is not known
C:\Users\akeeste\Documents\Software\GitHub\MHKiT\docs\source\ADCP_Delft3D_TRTS_example.ipynb:: WARNING: Pygments lexer name 'ipython3' is not known
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generating indices... genindex mat-modindex py-modindex done
copying linked files...
copying notebooks ... [100%] wecsim_example.ipynb
highlighting module code... [100%] pecos.utils
writing additional pages... search done
copying images... [100%] ../doctrees/nbsphinx/wecsim_example_31_0.png
copying static files... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 374 warnings.

The HTML pages are in ..

..\MHKiT-MATLAB\examples\environmental_contours_example.html
..\MHKiT-MATLAB\examples\loads_example.html
..\MHKiT-MATLAB\examples\power_example.html
..\MHKiT-MATLAB\examples\qc_example.html
..\MHKiT-MATLAB\examples\river_example.html
..\MHKiT-MATLAB\examples\SWAN_example.html
..\MHKiT-MATLAB\examples\tidal_example.html
..\MHKiT-MATLAB\examples\wave_example.html
..\MHKiT-MATLAB\examples\wecsim_example.html
..\MHKiT-MATLAB\examples\WPTO_hindcast_example.html
       10 file(s) copied.
Build finished. The HTML pages are in ..

[akeeste]

Noting for our records that many of the above warnings have historically been commonplace when building the docs but most of them shouldn't cause issues. It is difficult to use Sphinx to build both MATLAB and python docstrings. In the future, we'll look at automating the building process and creating an automated documentation test to ensure python/matlab docstrings are formatted without errors.