Tools for pull requests

[hkershaw-brown]

List of things to detect when people submit pull requests:

• if there are duplicate qtys added to qty files
• default qty file contains all known qtys (to DART not the universe)
• license header in each file
• svn info to remove, variations of:

   DART $Id$
   % <next few lines under version control, do not edit>
   % $URL$
   % $Revision$
   % $Date$
  

• conf.py version matches release (might have multiple pull requests in the release)
• source, revision, register_module

[hkershaw-brown]

@hkershaw-brown next pull request:
#804 (comment)

[hkershaw-brown]

removed action using tj-actions checkout https://github.com/NCAR/DART/security/dependabot/2

[hkershaw-brown]

Still have a lot of ../../../X.html links

make linkcheck takes a long time to run, too long for a pull request. Possible to only run on changed files to detect these?

make linkcheck ouptut

(assimilation_code/programs/obs_diag/oned/obs_diag: line   50) ok        ../../../../diagnostics/matlab/plot_rank_histogram.m
(models/CESM/doc/setup_guidelines: line  188) broken    ../../../assimilation_code/programs/obs_diag/threed_sphere/obs_diag.html - 
(assimilation_code/programs/obs_diag/oned/obs_diag: line   50) ok        ../../../../diagnostics/matlab/plot_evolution.m
(models/CESM/doc/setup_guidelines: line   81) broken    ../../../guide/controlling-files-output.html - 
(assimilation_code/modules/observations/obs_sequence_mod: line   14) broken    ../../../observations/obs_converters/README.md - 
(assimilation_code/programs/obs_seq_verify/obs_seq_verify: line  177) broken    ../../../assimilation_code/programs/obs_seq_coverage/obs_seq_coverage.html#example48x6 - 
(assimilation_code/programs/obs_seq_verify/obs_seq_verify: line  147) broken    ../../../assimilation_code/programs/filter/filter.html#Namelist - 
(models/NCOMMAS/readme: line  305) broken    ../../assimilation_code/location/threed_sphere/location_mod.html#get_close_obs - 
(models/NCOMMAS/readme: line  619) broken    ../../assimilation_code/location/threed_sphere/location_mod.html#get_close_maxdist_init - 
(observations/obs_converters/README: line  232) broken    ../../assimilation_code/location/threed_sphere/location_mod.html - 
(observations/obs_converters/README: line  232) broken    ../../assimilation_code/location/oned/location_mod.html - 
(models/MITgcm_ocean/create_ocean_obs: line   83) broken    ../../assimilation_code/modules/observations/obs_sequence_mod.html#Namelist - 
(observations/forward_operators/obs_def_ocean_mod: line  100) broken    ../../assimilation_code/modules/observations/obs_kind_mod.html#Namelist - 
(models/MITgcm_ocean/create_ocean_obs: line   20) broken    ../../assimilation_code/location/threed_sphere/location_mod.html#location_type - 
(observations/obs_converters/README: line  422) broken    ../../assimilation_code/programs/create_obs_sequence/create_obs_sequence.html - 
(observations/obs_converters/README: line  131) broken    ../../assimilation_code/modules/utilities/time_manager_mod.html#time_type - 
(models/MITgcm_ocean/create_ocean_obs: line   80) broken    ../../assimilation_code/modules/utilities/utilities_mod.html#Namelist - 
(models/CESM/readme: line  189) broken    ../../assimilation_code/programs/filter/filter.html#detailed-program-execution-flow - 
(observations/obs_converters/README: line  166) broken    ../../assimilation_code/programs/perfect_model_obs/perfect_model_obs.html - 
(assimilation_code/programs/create_obs_sequence/create_obs_sequence: line    7) ok        ../../../observations/obs_converters/README.rst
(observations/obs_converters/README: line  182) broken    ../../assimilation_code/programs/filter/filter.html#Inflation - 
(observations/obs_converters/MIDAS/MIDAS_to_obs: line   78) ok        ../../forward_operators/obs_def_upper_atm_mod.f90
(models/MITgcm_ocean/create_ocean_obs: line   26) broken    ../../assimilation_code/programs/filter/filter.html#Namelist - 
(models/coamps/readme: line  276) broken    ../../location/threed-sphere/location_mod.html#get_close_maxdist_init - 
(models/NCOMMAS/readme: line  636) broken    ../../assimilation_code/location/threed_sphere/location_mod.html#get_close_obs_init - 
(models/coamps/readme: line  293) broken    ../../location/threed-sphere/location_mod.html#get_close_obs_init - 
(models/pe2lyr/readme: line  317) broken    ../../location/threed_sphere/location_mod.html#get_close_maxdist_init - 
(models/ikeda/readme: line  388) broken    ../../location/oned/location_mod.html#get_close_obs - 
(observations/obs_converters/AVISO/AVISO: line   30) broken    ../../forward_operators/obs_def_ocean_mod.html - 
(assimilation_code/programs/obs_diag/oned/obs_diag: line   27) broken    ../../filter/filter.html#DetailedProgramFlow - 
(models/pe2lyr/readme: line  340) broken    ../../location/threed_sphere/location_mod.html#get_close_obs_init - 
(models/coamps/readme: line  315) broken    ../../location/threed-sphere/location_mod.html#get_close_obs - 
(assimilation_code/programs/gen_sampling_err_table/gen_sampling_err_table: line   10) broken    ../../modules/assimilation/assim_tools_mod.html#Namelist - 
(assimilation_code/location/channel/location_mod: line  550) broken    ../../modules/observations/obs_kind_mod.html#get_num_types_of_obs - 
(assimilation_code/programs/create_fixed_network_seq/create_fixed_network_seq: line   12) broken    ../../modules/observations/obs_sequence_mod.html#Namelist - 
(models/pe2lyr/readme: line   37) broken    ../../location/threed_sphere/location_mod.html#get_close_obs - 
(assimilation_code/programs/filter/filter: line  183) broken    ../../modules/assimilation/filter_mod.html#Modules - 
(guide/qceff-examples: line  187) broken    ../_static/papers/QCEFF_3_submitted.pdf - 
(assimilation_code/location/threed_sphere/location_mod: line   46) broken    ../../modules/assimilation/assim_tools_mod.html - 
(guide/assimilation-complex-model: line  112) broken    ../assimilation_code/modules/assimilation/assim_tools_mod.html#Namelist - 
(assimilation_code/modules/assimilation/filter_mod: line  456) broken    ../../programs/filter/filter.html#FilesUsed - 
( guide/inflation: line  114) broken    ../assimilation_code/modules/assimilation/filter_mod.html#Namelist - 
(guide/assimilation-complex-model: line   78) broken    ../assimilation_code/modules/assimilation/assim_tools_mod.html#Localization - 
(assimilation_code/programs/filter/filter: line  172) broken    ../../modules/assimilation/filter_mod.html#Namelist - 
(assimilation_code/modules/observations/obs_kind_mod: line  195) broken    ../../programs/preprocess/preprocess.html#Namelist - 
(guide/compiling-dart: line  167) broken    ../assimilation_code/programs/filter/filter.html - 
(guide/compiling-dart: line  169) broken    ../assimilation_code/programs/obs_diag/threed_sphere/obs_diag.html - 
(guide/compiling-dart: line  171) broken    ../assimilation_code/programs/obs_sequence_tool/obs_sequence_tool.html - 
(guide/compiling-dart: line  163) broken    ../assimilation_code/programs/create_fixed_network_seq/create_fixed_network_seq.html - 
(guide/compiling-dart: line  161) broken    ../assimilation_code/programs/create_obs_sequence/create_obs_sequence.html - 
(assimilation_code/modules/assimilation/quality_control_mod: line   18) broken    ../observations/obs_kind_mod.html#Namelist - 
(observations/obs_converters/README: line  223) broken    ../forward_operators/obs_def_mod.html - 
(guide/compiling-dart: line  165) broken    ../assimilation_code/programs/perfect_model_obs/perfect_model_obs.html - 
(models/CESM/readme: line   56) broken    ../cam-fv/readme.html - 
(models/CESM/doc/setup_guidelines: line  170) broken    ../readme.html - 
(observations/obs_converters/README: line  433) broken    even_sphere/README.html - 
(models/noah/readme: line   49) broken    dart_to_noah.html - 
(guide/compiling-dart: line  159) broken    ../assimilation_code/programs/preprocess/preprocess.html - 
( guide/mpi_intro: line   75) broken    filter_async_modes.html#async2 - 
(models/mpas_ocn/readme: line  131) ok        dart_to_model.f90
(assimilation_code/modules/assimilation/adaptive_inflate_mod: line  421) broken    filter_mod.html#Namelist - 
( guide/mpi_intro: line   72) broken    filter_async_modes.html#async0 - 
( guide/mpi_intro: line   79) broken    filter_async_modes.html#async4 -
...

[hkershaw-brown]

pytest added in #1044, runs only on changes to pytools directory.