Version 2.2.0, first real release of python based music box powered by micm #191
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* setting up a cmake structure for c++ * python box model iniital classes * added method for generating species config * added relative tolerance to spec config * added method to generate reaction config * added generateConfig documentation and todo solve function * added todo readfromjson function * added params to reaction * updated Reaction and getReactionConfig to handle A B D E and Ea paramaters * can mostly parse json file from UI * implemented skeleton logic for solver * extracted concentrations and reaction rates from evolving conditions * added initial reaction rates, need to verify * made conversion functions to shorten code * tested parsing with example that had every option * added other reaction types and refactored some code * fixed bug in species list * fixed bug in reaction list * generateReactionConfig accounts for the different types of reactions * added funciton to create micm solver based on config * added funciton to create micm solver based on config * working towards box model test * adds function to read config json and tests basic reaction * fixed solve to inc by seconds * convert time steps to seconds * updated solve with new time units * Changed readFromJson to readFromUIJosn * convert_pressure converts to Pa now * outputs results to file and creates file for initial test * reads species name from config * sets up test config and get analytical concentrations * aserts concentrations * fixed comment typo * fixed output outputted based on output time step * changed time in output to output step time * added hr to time conversion: * removed print stat * removed print statement * config files generatable * initial reaction rates added to generate config * reads species from json from camp_data * box model pr * handle cases without pressure and temperature in evolving conditions for UI parsing * able to recreate test config in UI, parse it, and use in python_test_1 * reads reaction list from config json * restructured functions * fixed missing reaction list param in from_config_JSON * can generate evolving_conditions.csv for config * implemented species and rate ordering in solve * moved where ordered arrays are computed * updated headers to match ordered array * fixed evolving conditions not setting attributes correctly * fixed unit issue with pressure for setting up evolving conditions * added reaction type prefixes in order_reaction_ratesz * changed evolving conditions to update in a while loop in case chem time step is greater than time between evolving conditions * updated python test 3 * creates test for chapman in python_test_3.py * renamed tests to be more descriptive * added test file for wall-loss * include base values for reactions, change C back to Ea * add species not present in initial conditions for order_species_concentration * removed unused files * removed unused files * created .whl for music_box package * make sure time in evolving conditions is float * check reaction names correctly for evolving conditions config, ensure floats for rate constants * added function to read from UI json string * removing fortran things, using musica python module, creating installation suitable for pypi * converting tests to pytest * correcting setup python? * adding a space * strategy * installing music_box in CI * newer checkout * pypi publish --------- Co-authored-by: Kyle Shores <[email protected]> Co-authored-by: Evan De la Garza <[email protected]> Co-authored-by: Evan De la Garza <[email protected]>
* does not add rel tolerance to species list * updates m according to temp and pressure * commented out concentration array override * changed Type to type * removes unecessary code
* fixed inital conditions for reaction rates * added handling for loss and emission in generating config * fixed chapman test * added scaling factors to config * changed initial conditions to be read and stored in a separate file
* added full gas phase test * edited tests
* documented music_box.py * documented music_box_conditions.py * documented evolving conditions * documented box model options * documented reaction list * documented reactions * documented species list
…iles (#154) * added documentations to missing functions * adds sphinx doc files in docs directory
* adding citation file * add names to the citation file --------- Co-authored-by: Evan De la Garza <[email protected]>
* Hello World from the new MusicBox main(). * Python main() is producing valid floating-point output. * Added command-line arguments. * Write out the solution. * Import music_box_logger the right way. * Move log statements into main(). * Removed realistic physical defaults, replaced with None. * Throw exception for None solver instead of Warning. * Removed ACOM Logger. Set up music_box operation as executable script and python command line. * Use argparse and configure it for key=value pairs. * Revise command-line arguments to configFile and outputDir. * pull smoke test action from other branch * Modified to look like the MusicBox template. * Display the working directory. * Removed redundant pip install. * Action test (#174) * listing debug information * ok actually printing wd * trying forward slashes * trying to join files independent of os slashes * removing csv file * Re-added file that was inadvertently deleted, and updated musica version tp 0.7.0 * Removed helper scripts from repository. * Removed another batch helper script. * Check for configFile parameter. Give error and example if not found. * Add key=value required parameter to argparse help. * Rename smoke test to CI Tests. Deleted test.yml. --------- Co-authored-by: Matt Dawson <[email protected]> Co-authored-by: Kyle Shores <[email protected]>
* setting up music box docs with our theme * adding logo * setting up new documentation * new logo
* correcting tests * removing commented out code * calling unit tests * requirements * changing directory
* testing package publishing * triggering * maybe wheels aren't necessary for this * fixing thing * don't think we need an sdist * lets have both, why not * adding both files to cache * removing push trigger * considering auto incrementing version * checking a version bump PR * maybe this * maybe it needs the branch name? * maybe this * trying to see if any changes are applied * debug * trying to get a PR to work * one more time * sure would like this to work * what is happening * i give up
* checking if autoformat action works * correcting action trigger
Co-authored-by: GitHub Actions <[email protected]> Co-authored-by: Kyle Shores <[email protected]>
* renaming docs, adding dockerfile, github action * Update .github/workflows/gh_pages.yml Co-authored-by: Jiwon Gim <[email protected]> * action triggers --------- Co-authored-by: Jiwon Gim <[email protected]>
…ces [Issue #177] (#180) * Remove all redundant `music_box_` from file names and updated references [Issue #177] * correcting relative imports * correcting more imports * renaming executable --------- Co-authored-by: Kyle Shores <[email protected]>
Co-authored-by: GitHub Actions <[email protected]>
Co-authored-by: GitHub Actions <[email protected]>
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