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Documentation Framework #1235

Merged
merged 38 commits into from
Oct 29, 2020
Merged

Documentation Framework #1235

merged 38 commits into from
Oct 29, 2020

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kshedstrom
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This replaces PR #1225

RTD: Update .readthedocs.yml for format two; allow the pdf to build
RTD: be sure to add UPDATEHTMLEQS=Y to RTD admin interface
Travis: Use makefile instead of calling binary directly
Travis: add python3-sphinix, remove doxygen as to build from specified version
Makefile: augment arguments to support a variety of doxygen and sphinx-build options
Makefile: move equation post processing from makefile to sphinx-build for RTD purposes
README/details: augment documentation; more needed
postProcessEquations.py: support doxygen 1.8.13
Fix some some src to update math formulas
Moving to doxygen 1.8.13 baseline broke clean pdf generation
There are still a lot of formatting issues to fix for the APIs/gh-pages and RTD. This PR should make the infrastructure for HTML generation at least functional.

kshedstrom and others added 30 commits August 19, 2020 18:05
- #1225 is showing lots of errors due to using a newer version of doxygen
- These doxygen mistakes exist in the current dev/gfdl branch and apparently
  are missed by the older versions we are using on mom6.readthedocs.io and
  locally.

Todo:
[ ] - Have the OBGC routines properly documented so we can replace the
      "Unknown" documentation in the generic_tracer stubs.
- Repair README & details pages
- Edit Makefile and .travis.yml to allow pointing to specific version of doxygen via github
- Testing PR for doxygen only right now
- Do not need to renumber equations in travis checks
- Allow a custom configuration file to be passed to make nortd via DOXYGEN_CONF
- Enable more sphinx type options to work at the doxygen level
- Set shebang for postPorcessEquations.py to python3
Rob Cermak and others added 7 commits October 26, 2020 19:37
- Makefile: Make sure pdf generation is in nonstopmode for doxygen latex.
- Makefile: Move from version 1.8.19 to 1.8.13 as baseline
- README: Remove bin/doxygen from file listing
- Enable post processing of equations in RTD
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codecov-io commented Oct 28, 2020

Codecov Report

Merging #1235 into dev/gfdl will decrease coverage by 0.05%.
The diff coverage is 32.03%.

Impacted file tree graph

@@             Coverage Diff              @@
##           dev/gfdl    #1235      +/-   ##
============================================
- Coverage     46.08%   46.03%   -0.06%     
============================================
  Files           214      224      +10     
  Lines         69399    71042    +1643     
============================================
+ Hits          31984    32702     +718     
- Misses        37415    38340     +925     
Impacted Files Coverage Δ
...g_src/external/GFDL_ocean_BGC/FMS_coupler_util.F90 0.00% <0.00%> (ø)
...fig_src/external/GFDL_ocean_BGC/generic_tracer.F90 0.00% <0.00%> (ø)
...c/external/GFDL_ocean_BGC/generic_tracer_utils.F90 0.00% <0.00%> (ø)
config_src/external/ODA_hooks/kdtree.f90 0.00% <0.00%> (ø)
config_src/external/ODA_hooks/ocean_da_core.F90 0.00% <0.00%> (ø)
config_src/external/ODA_hooks/ocean_da_types.F90 0.00% <0.00%> (ø)
config_src/external/ODA_hooks/write_ocean_obs.F90 0.00% <0.00%> (ø)
config_src/solo_driver/MESO_surface_forcing.F90 0.00% <0.00%> (ø)
config_src/solo_driver/user_surface_forcing.F90 0.00% <0.00%> (ø)
src/ALE/MOM_regridding.F90 31.47% <0.00%> (-0.17%) ⬇️
... and 229 more

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@adcroft adcroft merged commit 7e5231e into mom-ocean:dev/gfdl Oct 29, 2020
@kshedstrom kshedstrom deleted the docs_test branch October 30, 2020 20:09
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3 participants