[WIP] pilot parameter refactor #62

odunbar · 2022-02-10T01:16:41Z

Purpose of this PR

Relating to issues #57
Provides a toml format for other packages to use. Currently see

PR 83 on Clima/Thermodynamics
PR 55 on Clima/CloiudMicrophysics

Also we can now write re-readable log files

In this PR

Documentation! See the latest documentor build below.
New wrapper ParamDict{FT}around dictionary read from toml. Currently parametric on one type of all the values, provided when it is built (default is Float64). Construction:

create_parameter_struct(override_filepath, default_filepath; dict_type="alias",value_type=Float64) # builds with override and custom default provided
create_parameter_struct(override_filepath ; dict_type="alias",value_type=Float64) # builds, overriding the default from CLIMAParameters
create_parameter_struct(; dict_type="alias",value_type=Float64) # builds using only default in CLIMAParameters

Automated parameter logging on reading parameter values: (can do multiple parameters at once). At the call of this function, the type is enforced on the return values.

get_parameter_values!(pd::ParamDict, names, component; log_component=true) #logs component in pd
get_parameter_values(pd::ParamDict,names) # no logging in pd

writing the re-readable log file in log_parameter_information(pd::ParamDict,filepath). Example parameter tested in CloudMicrophysics.jl:

# initial parameter file
[molar_mass_water]
alias = "molmass_water"
value = 0.01801528
type = "float"

In this test, a copy of the parameters was created and stored in (1) Thermodynamics, (2) the general CloudMicrophysics, and (3) the specific 1-moment-based Microphysics scheme. Indeed the logfile shows this information below

# log file
[molar_mass_water]
alias = "molmass_water"
value = 0.01801528
type = "float"
used_in = ["Thermodynamics", "CloudMicrophysicsParameters", "Microphysics_1M_Parameters"]

The log_parameter_information(pd::ParamDict,filepath; warn_else_error="warn") will also throw warnings if a parameter is in the override file, but unused in the simulation. This works as parameters from the override file are checked for whether they have gained a "used_in" tag, if not found then an this is logged as a warning or error

From PR Enable get_parameter_values to deal with array-valued parameters #65, reading of array-type parameters
From PR [WIP] Read and write UQ parameters #68, reading and writing for calibration tools

TODO

still using alias based structs
still based on float, and array-of-float parameters

codecov · 2022-02-10T01:17:59Z

Codecov Report

Merging #62 (6370511) into main (bacec5a) will increase coverage by 12.32%.
The diff coverage is 94.33%.

❗ Current head 6370511 differs from pull request most recent head b3839b5. Consider uploading reports for the commit b3839b5 to get more accurate results

@@             Coverage Diff             @@
##             main      #62       +/-   ##
===========================================
+ Coverage   83.72%   96.04%   +12.32%     
===========================================
  Files           5        6        +1     
  Lines         172      278      +106     
===========================================
+ Hits          144      267      +123     
+ Misses         28       11       -17

Impacted Files	Coverage Δ
src/file_parsing.jl	`94.33% <94.33%> (ø)`
src/Planet/planet_parameters.jl	`100.00% <0.00%> (+35.29%)`	⬆️
src/UniversalConstants.jl	`100.00% <0.00%> (+71.42%)`	⬆️

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update bacec5a...b3839b5. Read the comment docs.

Project.toml

src/file_parsing.jl

test/array_parameters.toml

test/runtests.jl

charleskawczynski · 2022-05-17T00:49:43Z

Can we also add an example of what this will look like in practice? For example:

struct ParameterBox{FT}
alpha::FT
beta::FT
end

# construct / extract / use one

odunbar · 2022-05-17T01:13:34Z

I have docs pages for this already (https://clima.github.io/CLIMAParameters.jl/previews/PR63/parameter_structs/)
but i we could add something into the tests

src/file_parsing.jl

docs/src/parameter_structs.md

75: Add and apply JuliaFormatter r=charleskawczynski a=charleskawczynski Now that this revamp is getting near, and it involves code rather than many functions that just return constants, it makes sense to add the formatter. This PR adds and applies the JuliaFormatter. This should barely have any conflicts with #62, maybe a few small ones in the docs. Co-authored-by: Charles Kawczynski <[email protected]>

Enable get_parameter_values to deal with array-valued parameters - `get_parameter_values` extracts the requested parameter values and returns them as an array. The returned array contains the values corresponding to the given list of parameter names (unless a single scalar parameter is requested, in which case the function returns a float), regardless of whether these parameters are all of the same type. - E.g., given a list of parameter names ["scalar_param", "array_param"] with `scalar_param` having a scalar value and `array_param` being array-valued, the first element of the returned array will be a float, and the second element will be an array - Added more tests to `toml_consistency.jl` to check if parsing, extracting, and writing of array-valued parameters works. Also added a test for `merge_override_default_values` Enforce types and move `array_parameters.toml` to test folder Add V0 of TOML file parsing for UQ parameters Add functionality to write parameter ensembles to toml files Move docstrings above functions Add improvements and updates - save_parameter_ensemble now creates a separate subdirectory for each ensemble member, while the name of the saved parameter file after each ensemble Kalman update is the same for all members. Example: iteration_01/member_01/test_parameters.toml iteration_01/member_02/test_parameters.toml etc - correct saving of multidimensional parameters using parameter slices Move dict version of `write_log_file` from file_parsing.jl to file_parsing_uq.jl Within the CES API, `write_log_file` will take a parameter dictionary as input (rather than a parameter struct containing a parameter dictionary, as in the running-the-climate-model API). Since the two APIs will go separate ways in the future, the CES version of `write_log_file` should be located in `file_parsing_uq.jl`. added typo-checks for overrides, provides warnings or error on parameter logs slightly more revealing test documentation and guides Modify parsing of UQ parameters to work with new `ParameterDistribution` API Make tests work Add regularization flags Revise based on Ollie's comments, and remove print commands from tests moved toml and old files into directories parameter box example (as test set) Improve create_parameter_struct interface warn_else_error -> warn_or_error, and docs update Fix some docs, minor adjustments Apply formatter WIP Refactor

charleskawczynski

YESSS

odunbar · 2022-05-18T23:01:51Z

bors r+

bors · 2022-05-18T23:01:52Z

🔒 Permission denied

Existing reviewers: click here to make odunbar a reviewer

odunbar · 2022-05-18T23:03:56Z

bors r+

bors · 2022-05-18T23:12:00Z

Build succeeded:

odunbar mentioned this pull request Feb 10, 2022

[WIP] refactor parameters CliMA/CloudMicrophysics.jl#55

Closed

charleskawczynski reviewed Apr 29, 2022

View reviewed changes

Project.toml Outdated Show resolved Hide resolved

charleskawczynski reviewed Apr 29, 2022

View reviewed changes