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QCEFF Table #553

Merged
merged 131 commits into from
Nov 2, 2023
Merged

QCEFF Table #553

merged 131 commits into from
Nov 2, 2023

Commits on Oct 2, 2023

  1. draft program to experiment with reading table values into correspond… 

    …ing types
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  2. prototype table data file that uses CAM-FV QTYs

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  3. adding new subroutine init_qcf_table to return number of rows in table

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  4. Adding a new namelist variable to the assim_tools_nml

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  5. Adding QCF table type definitions to algorithm_info_mod

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  6. adding type defs to use statement for algorithm_info_mod in assim_too… 

    …ls_mod
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  7. Adding allocatable variables for table data, allocating after determi… 

    …ning size of table
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  8. New subroutine to read through the values in the QCF table and assign… 

    … them to the variables in the qcf_table_data_type
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  9. Removing qcf table data types from assim_tools_mod and reorganizing s… 

    …o that these type structs are only used in algorithm_info_mod
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  10. Fixing small inconsistencies/typos

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  11. moving the location of draft program outside /assimilation_code/modul… 

    …es/assimilation
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  12. Adding draft subroutine write_qcf_table to test that values are being… 

    … read in correctly; removed rowheaders argument from subroutines where not needed
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  13. replaicing conditionals and hardcoded values in probit_dist_info

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  14. using get_name_for_quantity to get generic quantity from integer index

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  15. Replacing conditionals and hard coded values with qcf_table_data in o… 

    …bs_inc_info subroutine
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  16. Replacing conditionals and hard coded values with qcf_table_data in o… 

    …bs_error_info subroutine
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  17. add subroutine to deallocate qcf table data structures

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  18. making dealloc subroutine available to assim_tools_mod

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  19. removing comment blocks of old code

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  20. Adding call to deallocate routine, removing unused var and old commen… 

    …ted code
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  21. Fixing typo in subroutine names

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  22. Moving the allocation and deallocation of qcf table data from assim_t… 

    …ools_mod to filter_main in filter_mod
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  23. uncommenting call to end_alg_info_mod

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  24. moving call to init_algortihm_info_mod out of conditional

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  25. Reorganizing the subroutines so that init_algorithm_info_mod is at th… 

    …e top of algorithm_info_mod
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  26. Adding qcf_table_listed logical and module_initialized checks

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  27. Moving location of qcf_table_listed check to before data access from … 

    …findloc
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  28. Using error_handler from utilities_mod; adding check for correct tabl… 

    …e version
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  29. adding qcf_table_file_listed logical to two remaining subrountines; w… 

    …ork with log_qcf_info
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  30. commenting out prints; remove these lines later

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  31. Moving initialize_modules call to be after read of filter_nml

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  32. Adding check that all QTYs in the table exist in DART using get_index… 

    …_for_quantity; adding checks that upper bounds are greater than lower bounds
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  33. Replacing open and close of qcf_table file with open_file and close_f… 

    …ile of utilities_mod - this fixes the issue with writing to the dart_log
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  34. Making quotations consistent - using single quote only

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  35. Adding checks for duplicate QTYs in the table

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  36. Switching to real(r8); experimenting in the log_qcf_table subroutine

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  37. reading in character strings from QCF table for filter_kind instead o… 

    …f ints
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  38. Reading in dist_type from the table as a character string instead of int

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  39. Fixing log format; cleaning code

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  40. Removing unnecessary files

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  41. Adding the yaml_to_table.py script and example yaml file qcf_table_te… 

    …mplate.yaml to the DART repo at /DART/assimilation_code/programs/qcf_table/. The location of these files in the repo may change
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  42. Fixing deallocation by adding conditional to check if data types were… 

    … allocated
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  43. Adjusting the YAML template file; removing trailing spaces from possi… 

    …ble_dist_types strings
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  44. Adding documentaion file to repo

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  45. Removing unused routines from utilities_mod use list

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  46. Adding &probit_transform_nml to input.nml files for lorenz 63 and 96 … 

    …- this will allow for the build and run lorenz github actions to pass
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  47. Removing the use_algorithm_info_mod logical from assim_tools_mod and … 

    …filter_mod
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  48. Fixing unintentional additions to lorenx 96 and 63 input.nml files; r… 

    …emoving use_algorithm_info_mod nml option
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  49. Adding spaces back in from unintentional removal

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  50. Adding &probit_transform_nml and qcf_table_filename option to model's… 

    … input.nml files (9var, am2, bgrid_solo)
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  51. Fixing missing commas in nml files

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  52. add test cases for reading qcf table

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  53. test script to check return codes for various qcf_table cases

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  54. remove stray /dev/null left in accidentally

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  55. add tests for various bounds options 

    currently the "lower bound only" test is failing
because the upper < lower check happens always rather then only when
you have two bounds
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  56. test for bounds set to false, but bounds values in the table

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  57. fix: need to check that a qty is bounded above and below before check… 

    …ing invalid bounds

otherwise missing_r8 -88888 value for the upper bound is "less than" the lower bound
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  58. fix: remove extra call to test_table read from runall.sh

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  59. replace kind with qty 

    kind is outdated terminolgy for quantity
#545 (comment)
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  60. add two tests for table read: incorrect filter kind, incorrect distri… 

    …bution

Currently the algorithm_info_mod does not catch these on table read
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Commits on Oct 3, 2023

  1. Fixing incorrect comments

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  2. Using HEADER_LINES parameter to replace hardcoded number

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  3. Changing the name of the logical qcf_table_listed to use_qty_defaults

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  4. Changing the name of qcf_table_data_type to algorithm_info_type

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  5. Removing old alternatives for algorithm_info_mod.f90

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  6. Moving the conversions for dist_type and filter_kind from string to i… 

    …nteger value to read_qcf_table, when the type is filled in
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  7. removing python script for yaml files - will be moved to a separate p… 

    …ull request
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Commits on Oct 4, 2023

  1. Changing the name of qcf_table_row_headers to specified_qtys

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  2. Adding &probit_transform_nml to remaining model input.nml files

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Commits on Oct 5, 2023

  1. chore: pin requirements for readthedocs

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Commits on Oct 9, 2023

  1. Removing rectangular_quadtrature and gaussian_likelihood_tails from t… 

    …he QCF table and obs_inc_info
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Commits on Oct 10, 2023

  1. Removed sort_obs_inc from the QCF table; removed code related to the … 

    …sort_obs_inc logical from filter_assim and obs_increment in assim_tools_mod.f90 and obs_inc_info in algorithm_info_mod.f90
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Commits on Oct 17, 2023

  1. Adding the code for sort_obs_inc into obs_increment_enkf

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  2. Logging the dist_type and filter_kind in their string formats instead… 

    … of ints
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  3. Updating the documentationc- adding info on the QCF and probit transf… 

    …orm tools to DART's main documentation page; removing outdated docs for using these tools
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  4. Fixing the link to the QCF doc page

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Commits on Oct 18, 2023

  1. Fixing some typos in the documentation

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  2. Revoving global filter_kind from assim_tools_mod and &assim_tools_nml… 

    …; making args for obs_inc_info intent(out)
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  3. Removing filter_kind from all input.nml files in the &assim_tools_mod… 

    … section
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  4. Fixing comment accidentally removed from MITgmc_ocean namelist

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Commits on Oct 19, 2023

  1. Adding documentation for the lorenz_96_tracer_advection examples with… 

    … Google Sheets
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  2. Doc fixes for lorenz_96_tracer_advection examples

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  3. More doc fixes

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Commits on Oct 23, 2023

  1. removing spread_restoration from the QCF table and related code from … 

    …assim_tools_mod
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  2. Moving the code for sort_obs_inc to the end of obs_increment_enkf sub… 

    …routine
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  3. Add call to finalize_utilities to developer_tests/qceff/test_table_re… 

    …ad.f90

Co-authored-by: Helen Kershaw <[email protected]>
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  4. Restoring lorenz_96_tracer_advection/readme.rst

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  5. Moving the QCF examples doc to /guide

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  6. Removing old comment from obs_inc_info

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  7. Removing another old comment from obs_inc_info

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  8. Removing old comment from assim_tools_mod

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  9. Small fixes to the main DART doc page (index.rst)

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  10. Adding earlier link to the QCF docs

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  11. Adding the pre-made .csv files for the lorenx 96 tracer examples to /… 

    …lorenz_96_tracer_advection/work. Removing the information describing how to download the .csv files from Google Sheets from the QCF examples doc
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Commits on Oct 24, 2023

  1. Making the table version number be a parameter, not a magic number

    @mjs2369
    mjs2369 committed Oct 24, 2023
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  2. Removing unnecessary setting of the bounds before the call to obs_inc… 

    …_info
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    mjs2369 committed Oct 24, 2023
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  3. Fixing extended link in the docs

    @mjs2369
    mjs2369 committed Oct 24, 2023
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  4. Fixing the formatiing of code blocks in the docs

    @mjs2369
    mjs2369 committed Oct 24, 2023
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  5. MISSING_R8 is now all in capitals

    @mjs2369
    mjs2369 committed Oct 24, 2023
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  6. Fixing misleading comment placement

    @mjs2369
    mjs2369 committed Oct 24, 2023
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  7. Using the public parameters from algorithm_info_mod.f90 for compariso… 

    …ns with filter_kind value
    @mjs2369
    mjs2369 committed Oct 24, 2023
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  8. Fixing and removing outdated comments

    @mjs2369
    mjs2369 committed Oct 24, 2023
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Commits on Oct 25, 2023

  1. Removing one last reference to spread_rest from the QCF table docs

    @mjs2369
    mjs2369 committed Oct 25, 2023
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Commits on Oct 26, 2023

  1. fix: finalize utilities called last & need to be in use statement

    @hkershaw-brown
    hkershaw-brown committed Oct 26, 2023
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  2. Merge branch 'quantile_methods' into qcf_table

    @hkershaw-brown
    hkershaw-brown committed Oct 26, 2023
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  3. updated developer tests for qceff to match latest qcf_table 

    removed columns:
rectangular_quadrature	gaussian_likelihood_tails	sort_obs_inc	spread_restoration
    @hkershaw-brown
    hkershaw-brown committed Oct 26, 2023
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  4. remove unused variable NORMAL_DISTRIBUTION

    @hkershaw-brown
    hkershaw-brown committed Oct 26, 2023
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  5. swap magic number 8 for filter_kind paramter

    @hkershaw-brown
    hkershaw-brown committed Oct 26, 2023
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  6. fix qcf_table_lower_bound_only.txt to match latest 

    Currently the when lower_bound=.false. the lower bound is set the value lower_bound rather MISSING_R8
    @hkershaw-brown
    hkershaw-brown committed Oct 26, 2023
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  7. store specified qtys as integers because qtys in dart are integer par… 

    …ameters

replace kind with qty
    @hkershaw-brown
    hkershaw-brown committed Oct 26, 2023
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  8. Comment tidy: kind, type, qty cleanup and remove out-of-date comment 

    whitespace tidy for readability
    @hkershaw-brown
    hkershaw-brown committed Oct 26, 2023
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Commits on Oct 27, 2023

  1. Merge branch 'quantile_methods' into qcf_table

    @hkershaw-brown
    hkershaw-brown committed Oct 27, 2023
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  2. doc: describe the example qcf table files for the lorenz_96_tracer ex… 

    …amples
    @hkershaw-brown
    hkershaw-brown committed Oct 27, 2023
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  3. doc: how-to for qcf table 

    moved QCEFF out of getting started.

replaced Quantile Conserving and Probit Transform Filtering Tools
with Quantile Conserving Ensemble Filtering Framework because the
docs refer to QCEFF
    @hkershaw-brown
    hkershaw-brown committed Oct 27, 2023
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Commits on Oct 30, 2023

  1. doc-fix: example A QTY_TRACER_CONCENTRATION lower bound = 0

    @hkershaw-brown
    hkershaw-brown committed Oct 30, 2023
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  2. probit_transform defaults 

    fix_bound_violations        = .false.,
use_logit_instead_of_probit = .false.,
do_inverse_check            = .false.,

removed duplicate &probit_transform_nml
from lorenz_96_tracer_advection input.nml
    @hkershaw-brown
    hkershaw-brown committed Oct 30, 2023
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  3. two qtys are bounded

    @hkershaw-brown
    hkershaw-brown committed Oct 30, 2023
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  4. Jeff edits for index.html 

    defaults: filter_kind EAKF, dist_type NORMAL_DISTRIBUTION
code changed to match Jeffs edits.
    @hkershaw-brown
    hkershaw-brown committed Oct 30, 2023
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  5. remove out-of-date cam-fv input.nml for testing quantile_methods

    @hkershaw-brown
    hkershaw-brown committed Oct 30, 2023
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  6. docs: sort_obs_inc only applied for ENKF, and default is true

    @hkershaw-brown
    hkershaw-brown committed Oct 30, 2023
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  7. doc: spread_restoration not available in this version

    @hkershaw-brown
    hkershaw-brown committed Oct 30, 2023
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  8. doc: grammar

    @hkershaw-brown
    hkershaw-brown committed Oct 30, 2023
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  9. doc: remove filter_kind from assim_tools_mod namelist info 

    update error message (filter_kind not a namelist option)
    @hkershaw-brown
    hkershaw-brown committed Oct 30, 2023
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  10. rename all things qcf to qceff 

    The offical name:
Quantile-Conserving Ensemble Filter Framework
    @hkershaw-brown
    hkershaw-brown committed Oct 30, 2023
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  11. developer test for lower case in qceff table 

    currently failing
    @hkershaw-brown
    hkershaw-brown committed Oct 30, 2023
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  12. developer test for lower case dist_type 

    currently failing, need to_upper on all string inputs in algorithm_info_mod
    @hkershaw-brown
    hkershaw-brown committed Oct 30, 2023
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Commits on Oct 31, 2023

  1. fix: upper case for string inputs 

    changed if statements to case, so to_upper called once before the
case statement
    @hkershaw-brown
    hkershaw-brown committed Oct 31, 2023
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  2. doc-fix: change code block for read_input_state_from_file to match th… 

    …e text
    @hkershaw-brown
    hkershaw-brown committed Oct 31, 2023
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  3. fix: qceff_table_filename now a namelist option in algorithm_info_mod 

    This is so perfect_model_obs and filter_mod can use the algorithm_info_mod

remove obsolete use_algorithm_info_mod namelist option from perfect_model_obs
perfect model obs initialize and end algorithm_info_mod

qceff_table_filename removed from filter_nml
algorithm_info_mod example.nml

update example.nmls to match latest options (removed filter_kind)
adding algorithm_info_nml to model input.nmls

The developer_tests/qceff will not work with this (passing in a filename)
    @hkershaw-brown
    hkershaw-brown committed Oct 31, 2023
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Commits on Nov 1, 2023

  1. Fixing typo in the qceff-examples doc

    @mjs2369
    mjs2369 committed Nov 1, 2023
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Commits on Nov 2, 2023

  1. Updating the CHANGELOG and version # in conf.py

    @mjs2369
    mjs2369 committed Nov 2, 2023
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