Consider using cmake-format cmake-lint for pre-commits #1
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scharlton2
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Apr 10, 2023
b1f9657e 40 add bmibmi to bmiphreeqcrm and update swig interfaces (#44) f02a1289 Merge pull request #43 from scharlton2/42-undefined-symbol-_zn9phreeqcrm12getviscosityerst6vectoridsaidee 176265c7 ifdef'd out GetViscosity decalaration ba5eff55 Merge pull request #41 from dlparkhurst/bmi-f90 74bb6fe2 private UpdateBMI 47ed834a Merging from master Merge remote-tracking branch 'origin/master' into bmi-f90 ad31056c documenting c++ BMI 3914eca6 34 add pkg config to autotools and cmake distribution (#36) be9a12fa Merge pull request #39 from dlparkhurst/bmi-f90 120819d0 Scott's fixes 5a54a06c Merge pull request #37 from dlparkhurst/bmi-f90 b6dee735 Fixed unhandled enum warnings Renamed BMI_not_implemented.F90 to BMI_not_implemented.inc Added @todo for asserts that fail during ctest c4eaf6be Working on PR #37 33892817 fixed compiler warnings except NAN 4512421c fixed CMakeLists to include BMI_not_implemented.F90 a685d853 fixed bug in AdvectBMI_f90, fixed include file name 9ea68797 added dummy functions for all non-implemented methods 161e8566 Added Fortran pointers 895425c4 runs all the test cases, I'll have to check whether they are right. 58a2dfb0 fixed bug with rm2bmiupdate 961a2488 runs AdvectBMI_cpp.cpp 7c476c22 compiles. Finally figured out how to call the function pointers. 3143686f need to figure out how to run the functions adfd2027 retrieved AdvectBMI_cpp.cpp. Code compiles, start debug b9e47a22 removed static declaration. need to retrieve AdvectBMI_cpp.cpp 5118117c 4 unresolved references? 529a9bee moved enum to RMVARS.h bbd36de7 circular header file problem 653fdb2a PhreeqcRM.h in VarManager.h and VarManager.h in PhreeqcRM.h b274e554 circular references 126ebeda finished the _Var functions. Need to switch from _var and bmi_instance to new _Var and VarManager. 617bd89d through time_var. eight to go 376fed37 through gridcellcount 72b1ba12 Working on Vars, through FilePrefix, but have templates now ede8914a long way to go f6afcea5 reorganizing with VarManager class 787c57f1 All methods for C++ BMI are defined. Need to sort out SetValue and GetValue. Test. Finish F90 BMI. 597f9573 working on get_value_ptr for C++ and Fortran 71753f89 merged from master through bmi-reorg e14ed79c merging 3/26 to bmi-reorg; then merge bmi-f90 Merge remote-tracking branch 'origin/master' into bmi-reorg 8d648fc7 Closes usgs-coupled/phreeqcrm#32 (#33) ebf3fcdf had not checked in BMI_interface_F.h cbf328f8 Have getters, setters, and other grid functions left to do (and documentation) c0879cb9 implementing correct BMI F90. Through time functions. test cases run 6454bfd7 implementing correct BMI F90. Test cases run 9bbcbc99 reorganizing and adjusting for bmi documentation c7ee70dc renamed BMI_methods.h f9b48013 runs all tests ba784fa9 VS2022 & new Intel Fortran. Compiles and runs F90 BMI test case. f5997bd1 can't find the Fortran methods? 52997c17 BMI_interface 1270d87d changed all double precision to real(kind=8) in all files. Compiles and runs test cases. e314056d Merge branch 'dlparkhurst-bmi-reorg' 82859c7e Ran: pre-commit run --all-files bec6e176 Merge branch 'bmi-reorg' of https://github.com/dlparkhurst/phreeqcrm-bmi into dlparkhurst-bmi-reorg 1ba7c513 Cleaned up Fortran GetVarType. f36e7644 all test cases run. Added BMI_Create for F90 29689d21 InputVarNames and OutputVarNames work. Runs AdvectBMI_f90.F90 to completion. Need to work on Fortran GetVarType. 6fb16ecf fixing bugs aff8ac92 Something is broken for F90. 96fdc1bd need to fix logic of Info and GetFn a101bf35 bmi_methods.h has C++ BMI documentation 024a3f2b removed old C++ BMI routines, BMI_Methods.cpp and .h. Now using new version for Fortran (modified RM_BMI_interface_F.cpp to use new BMI methods). Need to keep BMI_Methods.h for C++ documentation. b7942285 Added Instances to BMIPhreeqcRM 8300fa88 Merge pull request #30 from scharlton2/29-configure-enable-fortran-test-with-yaml-cpp-fails-make-check 0989c870 Fixed ERROR: files left in build directory after distclean: d436f5ee Fixed RM_BMI_Initialize seems the call to trim stripped the c_null_char by GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 fc427dfc Fixed make check 3cf23344 C++11 fix for macos c3d966b6 added BMIPhreeqcRM.cpp and .h to CMake. Separated BMI_methods.h as a #include in PhreeqcRM. Ultimately, BMI_methods should be eliminated. Compiles and runs test cases using new BMIPhreeqcRM methods. 6b108118 Closes usgs-coupled/phreeqcrm#29 2f1f609a AdvectBMI_cpp.cpp runs to completion with BMIPhreeqcRM. Fixed bugs with function map, logic in SetVar and GetVar. Should be equivalent to previous version in the variables for get and set. Will add more variables with time. 3661fd61 ready for testing 11112106 nearly done with original vars 93b035e5 starting on _vars, modifying BMI_Var to have Nbytes and Itemsize. e9f7a86f Tidied a bit, ready to start on the _var methods 77cfae74 All BMI functions are defined. Compiles, but completely untested c3ef0728 beginning to reorganize BMI 39bce39a Merge pull request #28 from dlparkhurst/26-logical-kind-warnings-with-gfortran b4906331 Closes usgs-coupled/phreeqcrm#26 0d773484 Merge remote-tracking branch 'origin/master' into bmi-working a049065d roughed in AdvectBMI_py.py, not working fd611aed Merge pull request #25 from scharlton2/bmi-working d11bbc19 Merge remote-tracking branch 'dlpark/bmi-working' into bmi-working 82052ba5 removed IntVector and DoubleVector 2142702d wrote the Python YAML documentation a43f3fd1 syncing AdvectBMI_xxx.yaml 5a97824c Latest test output files ab533ead Getting Python yaml source and test case 170ad39d Mostly doxygen updates 77724104 Merge remote-tracking branch 'dlpark/bmi-working' into bmi-working 4ed9eddb Finishing up documentation of Python PhreeqcRM bindings bf926632 reformatted paragraphs 1b68510d Working on bmi 916978c9 PhreeqcRM.i compiles f6971034 almost ready to add to .i file 1e641bba python documentation 81569491 fixing python documentation 2e5b0852 indentation ff9cb9e6 emaced the method documentation 1d09244a Updated Makefile.am for pyfragments.swg.in 78142ab9 Can now debug on windows (no numpy) 8c0b8f98 Moved fortran file ee4a3e09 Simple advect should run to nxyz not nxyz/2. Add BMI_Var.h to RM_BMI_interface_F.cpp 637ca8a0 Working on pr #24 95d9e7fb Merge pull request #1 from dlparkhurst/bmi-working f1d1105e merged with master on trunk 223de822 cleaning Doxygen as I can 18acab9f finished documentation, but needs cleanup. Not sure how to document polymorphism in Fortran. Need to get YAML Fortran Doxygen to appear. ce86c074 finished YAML F90 documentation. Need to check c4d92f30 working through YAML_interface.F90 documentation f0afac12 Master swig python (#23) 81d71e34 documenting and fixing bugs ef5b83a1 Finished renaming files and updating CMakeLists. Fixed a couple bugs in AdvectBMI_f90 d5d4cefb renaming to YAML_interface 97706607 Added --output-on-failure to ctest 90ef63c4 put back file accidentally deleted from CLists 1dc4f91d moved RM_BMI_interface.F90 into RM_interface.F90. Makes Doxygen work and avoids some preprocessor bug. 13837b0c F90 YAML works. The preprocessor directive in RM_BMI_interface.F90 is not working. Added other ifdef USE_YAML. No YAML fails because of the preprocessor error. bab47170 works on the test cases including F90 yaml. Need to document F90 YAML and update cmakelists bbe3ffdf added WriteYAMLFile_f90, need to test. Need to update CMakelists 1b3cc6fb YAML F90 bindings done, start checking bf0cbc27 working on Fortran bindings to YAMLPhreeqcRM. Last file is one third done--YAMLPhreeqcRM.F90 905e70cd updated documentation for GetDensity and GetSaturation 54d4ccae tweak 5e90b8dc Final? touches on Doxygen 1b374167 cleaning up documentation 28b17d07 Moved RM_ (no BMI_) to RM_interface.F90, removed RM_ to just GetGridCellCountYAML for Fortran. b0816d5f Will eventually add RM_BMI_interface.F90 to RM_interface.F90 e9413f89 Going to try adding all defs to RM_interface.F90 1ae57981 Going to try adding all defs to RM_interface.F90 401fe2ca reformatted 5a4c10ae F90 GetValue documented ad1e699b F90 GetValue documented 9e7ef5ec Fixed my screwup with void* F90 GetValue and SetValue. Void * version is needed. MadeNthSelectedOutputUserNumber 1 based for Fortran. d8f3bc7a working on doxygen ff51de03 checkin 81d9bf6b Used INCLUDE for BMI Fortran. Continued documenting 6821163e documenting, am going to try to make F90 files smaller f1f38ec7 Need to update BMI documentation for C++ and Fortran d843d409 revised BMI_GetValue and BMI_SetValue to eliminate void* in the C++ version. Fortran still calls a void* version. Revised AdvectBMI_cpp to use the revised methods. 77d976e5 finishing up AdvectBMI_f90 and AdvectBMI_cpp 3822f64d need to add tests for setters 44672f84 Merge branch 'usgs-coupled:master' into bmi-working 491b380c merged fortran branch into bmi-working 777af151 Merge remote-tracking branch 'origin/bmi-working' into bmi-working Scott has updated master fork. Propogating changes here. 683882ee working on testing advectbmi_f90. Added RM_GetPorosity and RM_GetPressure. Modified GetValue and SetValue to ensure dimensions are correct. Added benefit that allocate can occur in GetValue.Need to finish BMI_testing. Still need to document Fortran methods in RM_BMI_Interface_F.F90 c24c7288 started BMI_testing for F90. Started documentation for RM_BMI_interface.F90. Instead, I am going to work on the getters and setters to handle allocation. Also added inputvarnames and output varnames. 0c588c58 cleaned up AdvectBMI_cpp a little. Made case independent 6daa2a66 AdvectBMI_f90 output files 1e9309bd AdvectBMI_f90 is running c6b4fe7b cleaning up RM_BMI_interface.F90 8f8be7cb Working through AdvectBMI_f90.F90 0902e751 Starting on AdvectBMI_f90.F90 test case 5457017e Finished Fortran methods. Need to translate AdvectBMI_f90.F90 e89b47e3 Working on Fortran BMI b443b57a Working on Fortran BMI 604c6480 added GetGridCellCountYAML to example code git-subtree-dir: src/phast/PhreeqcRM git-subtree-split: b1f9657e932a0fe84b159d37a0e5acfb0cf38a12
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