Remove musica-core dependency #51
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K20shores
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Mar 4, 2024
mattldawson
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Mar 20, 2024
* add TS1 and TSMLT configuration to examples * add new data sets for WACCM * fix memory leak in tests * add updated CFC cross section datasets * run example test in sub folders * copy data into example test folders * reorganize temperature based cross section * draft taylor series temperature parameterization * add taylor series param test * adjust grid merging logic * finish BRONO2 config and tests * fix MPI code * draft burkholder parameterization and tests * add range override to quantum yields * finish HO2NO2 config and tests * update TSMLT config example * fix example configurations * fix ch4 example config * add ch3cl data set and configuration * add SO2 data set * Updates and tests for O2 photolysis (#38) * stub test of LUT LA-SRB calcs * update lasrb test conditions * add od and xs calcs to LUT LA-SRB test * fix memory issues in tests * finish LA-SRB LUT comparison test * Add H2SO4 and NO datasets, configurations, and algorithms for WACCM (#41) * draft h2so4 quantum yield and test * add h2so4 qy test * add data and config for H2SO4 and NO * Add N2O5 algorithms and data sets for WACCM/TSMLT (#43) * fix bad jo2 config in ts1 example * add N2O5 algorithms and datasets for WACCM * fix pack/unpack for temperature based cross section * add acetone calcs for WACCM (#45) * add acetone calcs for WACCM * fix uninitialized variable and air density in tests * add branch options to acetone quantum yields * Add YAML option for configuration files (#48) * add YAML config option * add yaml to json run comparison tests * update to new musica-core release * Add ability to calculate heating rates for photolysis reactions (#50) * draft heating rates class and tests * finish heating rate tests * add heating rate output to driver, and include in TS example * Remove musica-core dependency (#51) * merge in musica-core dependencies * don't run tests in parallel * remove unneeded utility modules * remove io functions from string_t * remove debug output from tests to reduce log file size * update valgrind suppressions for MPI * update valgrind suppressions * fix valgrind suppression format error * remove wildcards from valgrind supresssion error types * add valgrind suppression * compile for gcc-13 (#53) * compile for gcc-13 * excluding oldtuv when using gcc 13.2 * removing cmake debug message * trying to add a gcc action * syntax error * isntalling netcdff * trying to test multiple gcc versions * installing numpy * scipy * using better thing * separating build into docker and gcc (#54) * separating build into docker and gcc * fixing pages build * run tests in serial * not running tests in parallel for focker * making sure memcheck happens * adding ctiation file (#55) * adding ctiation file * only adding software citation * syntax * more syntax * maybe now? * correcting authors * ... * or now * duplicate key * *marge noise* * trying to update url * Fix bug in map test with OpenMP (#56) * fix openmp bug in map test * fix map test for non-openmp builds * prepare for 0.8.0 release --------- Co-authored-by: Kyle Shores <[email protected]>
mattldawson
added a commit
that referenced
this pull request
Mar 20, 2024
* add TS1 and TSMLT configuration to examples * add new data sets for WACCM * fix memory leak in tests * add updated CFC cross section datasets * run example test in sub folders * copy data into example test folders * reorganize temperature based cross section * draft taylor series temperature parameterization * add taylor series param test * adjust grid merging logic * finish BRONO2 config and tests * fix MPI code * draft burkholder parameterization and tests * add range override to quantum yields * finish HO2NO2 config and tests * update TSMLT config example * fix example configurations * fix ch4 example config * add ch3cl data set and configuration * add SO2 data set * Updates and tests for O2 photolysis (#38) * stub test of LUT LA-SRB calcs * update lasrb test conditions * add od and xs calcs to LUT LA-SRB test * fix memory issues in tests * finish LA-SRB LUT comparison test * Add H2SO4 and NO datasets, configurations, and algorithms for WACCM (#41) * draft h2so4 quantum yield and test * add h2so4 qy test * add data and config for H2SO4 and NO * Add N2O5 algorithms and data sets for WACCM/TSMLT (#43) * fix bad jo2 config in ts1 example * add N2O5 algorithms and datasets for WACCM * fix pack/unpack for temperature based cross section * add acetone calcs for WACCM (#45) * add acetone calcs for WACCM * fix uninitialized variable and air density in tests * add branch options to acetone quantum yields * Add YAML option for configuration files (#48) * add YAML config option * add yaml to json run comparison tests * update to new musica-core release * Add ability to calculate heating rates for photolysis reactions (#50) * draft heating rates class and tests * finish heating rate tests * add heating rate output to driver, and include in TS example * Remove musica-core dependency (#51) * merge in musica-core dependencies * don't run tests in parallel * remove unneeded utility modules * remove io functions from string_t * remove debug output from tests to reduce log file size * update valgrind suppressions for MPI * update valgrind suppressions * fix valgrind suppression format error * remove wildcards from valgrind supresssion error types * add valgrind suppression * compile for gcc-13 (#53) * compile for gcc-13 * excluding oldtuv when using gcc 13.2 * removing cmake debug message * trying to add a gcc action * syntax error * isntalling netcdff * trying to test multiple gcc versions * installing numpy * scipy * using better thing * separating build into docker and gcc (#54) * separating build into docker and gcc * fixing pages build * run tests in serial * not running tests in parallel for focker * making sure memcheck happens * adding ctiation file (#55) * adding ctiation file * only adding software citation * syntax * more syntax * maybe now? * correcting authors * ... * or now * duplicate key * *marge noise* * trying to update url * Fix bug in map test with OpenMP (#56) * fix openmp bug in map test * fix map test for non-openmp builds * prepare for 0.8.0 release * Update publish-package.yml --------- Co-authored-by: Kyle Shores <[email protected]>
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Moves needed utility modules from
musica-coretosrc/utiland removesmusica-coreas a dependency of TUV-x. Also updates build/container scripts to always useyaml-cppfor both JSON and YAML, removingjson-fortranas a dependency.Closes #49