Merge branch 'main' into wrf-fresh

.gitignore

@@ -189,6 +189,7 @@ stacktest
 obs_rwtest
 test_quad_irreg_interp
 test_quad_reg_interp
+test_table_read
 test_ran_unif
 
 # Directories to NOT IGNORE ... same as executable names

CHANGELOG.rst

@@ -22,6 +22,89 @@ individual files.
 
 The changes are now listed with the most recent at the top.
 
+**January 11 2024 :: QCEFF. Tag v11.0.0**
+
+Nonlinear and Non-Gaussian Data Assimilation Capabilities in DART
+
+- Adds a Quantile-Conserving Ensemble Filtering Framework (QCEFF) to DART.
+  Publications: `QCEFF part1 <http://n2t.net/ark:/85065/d7mk6hm4>`_,
+  `QCEFF part 2 <http://n2t.net/ark:/85065/d7nv9pbt>`_.  
+
+- The default QCEFF options are EAKF, normal distribution (no bounds).
+
+- User interface changes:
+
+  - filter_kind is now a per-qty option through QCEFF table.
+
+  - Two new required namelists (add to input.nml files):
+
+    - probit_transform_nml
+    - algorithm_info_nml
+
+  - assim_tools_mod namelist:
+
+    - sort_obs_inc namelist option applied to ENKF only, so default is now .true.
+    - ``spread_restoration`` is not supported in this version
+
+  - algorithm_info_mod QCEFF options read at runtime from .csv or .txt file
+
+
+- New probability distribution modules:
+
+  - beta_distribution_mod *contributed by Chris Riedel*
+  - bnrh_distribution_mod (bounded normal rank histogram)
+  - gamma_distribution_mod
+  - normal_distribution_mod
+
+  -  probit_transform_mod 
+  -  distribution_params_mod
+
+- Update to lorenz_96_tracer_advection:
+
+  - positive_tracer
+  - more tracer namelist options available and changed defaults
+  - updated perturbation routine
+  - bug-fix: real(r8) rather than real(i8)
+
+- Fix: obs_def_1d_state_mod (oned forward operators):
+
+  -  For non-integer powers, fix up values for negative bases
+
+- Documentation:
+
+  - main page section on Nonlinear and Non-Gaussian Data Assimilation Capabilities in DART
+  - QCEFF instructions: Quantile-Conserving Ensemble Filter Framework
+  - Example to work through: QCEFF: Examples with the Lorenz 96 Tracer Model
+
+**January 9 2024 :: Derecho CLM-DART. Tag v10.10.1**
+
+- CLM-DART scripting updated for Derecho.
+- CLM-DART SourceMods packaged with DART.
+- Reinstituted both 'complete' and 'single_year' datm streamlist files in shell scripts
+  due to delays when initializing the CAM reanalysis files through campaign/collections directory.
+
+bug-fixes:
+
+- Fixed format statement in assert_mod to conform to Fortran standards.
+- Fixed debugging output for failed forward operators.
+
+doc-fixes:
+
+- Remove broken link for register for dart.
+
+**December 13 2023 :: Developer tests and bug fixes. Tag v10.10.0** 
+
+- new developer tests to run all builds for all compilers on NSF NCAR machine
+  Derecho.
+- removed redundant nc_check routine from utilities_mod in favor of 
+  netcdf_utilities_mod::nc_check
+- Improved default thinning options for AIRS L2 converter.
+
+bug-fixes:
+
+- AIRS L2 converter message prints correct number of obs.
+- MOM6 model_mod .eqv. used for logical comparison to conform to Fortran standard.
+
 **December 1 2023 :: Bringing DART documentation in accordance with NSF Policy. Tag v10.9.2**
 
 - doc-fixes:
@@ -45,13 +128,26 @@ The changes are now listed with the most recent at the top.
 bug-fixes:
 
 - filter_mod.dopperlerfold in sync with filter_mod
-- unnecessary loop removed from Mersenne twister developer test
+- unnecessary loop removed from Mersenne twister developer test 
 
 doc-fixes:
 
 - rename assim_model_mod.rst to match the module
-- fix various Sphinx warnings and broken link
-
+- fix various Sphinx warnings and broken link 
+
+**November 2 2023 :: QCEFF Input Table. Tag v11.1.0-alpha**
+
+- The QCEFF input table allows for the specification of QCEFF/probit
+  input options, per QTY, at runtime.
+- This replaces the functionality of using an algorithm_info_mod specific
+  to the model, which meant editing algorithm_info_mod.f90 to specify
+  which distribution should be used for which quantity.
+- The algorithm_info_mod files for the lorenz_96_tracer_advection model
+  examples have been replaced with set QCF tables (all_bnrhf_qcf_table.csv,
+  all_eakf_qcf_table.csv, state_eakf_tracer_bnrhf_qcf_table.csv,
+  neg_qcf_table.csv) and can be found in lorenz_96_tracer_advection/work.
+- Removed the ‘global’ version of filter_kind from assim_tools_mod.f90
+  and the &assim_tools_nml
 
 **October 5 2023 :: WRF-DART tutorial diagnostic section. Tag v10.8.5**
 

README.md

@@ -1,5 +1,6 @@
 [![GitHub forks](https://img.shields.io/github/forks/NCAR/DART?style=social)](https://github.com/NCAR/DART/network)
 [![GitHub release](https://img.shields.io/github/v/release/NCAR/DART)](https://github.com/NCAR/DART/releases/latest)
+[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
 [![Documentation Status](https://readthedocs.org/projects/dart-documentation/badge/?version=latest)](https://dart-documentation.readthedocs.io/en/latest/?badge=latest)
 
 ![DARTlogo](guide/images/Dartboard7.png)
@@ -23,8 +24,6 @@ DART is available through GitHub. To download the latest version of DART:
 git clone https://github.com/NCAR/DART.git
 ```
 
-To register for DART and view the terms of use, click on [register for DART](https://www2.cisl.ucar.edu/software/dart/download).
-
 #### Citing DART
 
 To cite DART, please use the following text:

assimilation_code/modules/assimilation/adaptive_inflate_mod.f90

@@ -722,8 +722,6 @@ subroutine update_varying_state_space_inflation(inflate, inflate_mean, inflate_s
 logical,                     intent(in)    :: inflate_only
 
 real(r8) :: gamma, ens_var_deflate, r_var, r_mean
-real(r8) :: diff_sd, outlier_ratio
-logical  :: do_adapt_inf_update
 
 if(inflate_mean <= 0.0_r8 .or. inflate_sd <= 0.0_r8) return