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Enhance CI, migrate to CMake, and improve documentation and tests#125

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jameslehoux merged 22 commits intoworkingfrom
master
Mar 7, 2026
Merged

Enhance CI, migrate to CMake, and improve documentation and tests#125
jameslehoux merged 22 commits intoworkingfrom
master

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Chore(ci): Integrate clang-tidy static analysis into CI pipeline
Migrate build system from GNUmakefile to CMake for improved workflows
Move test drivers to tests/ directory and update build systems
…-setup-7bMLw

Enhance CI workflows, input validation, and add dry run mode
Enhance CI workflows, input validation, and implement dry run mode
Implement multi-phase transport coefficient support and tests
Add config-driven physics type support for transport properties
Integrate Catch2 and expand PhysicsConfig unit test coverage
Implement JSON output for pipeline interoperability and BPX support
Add code coverage tracking and Codecov integration to CI
Fix Codecov and build badges to reference master branch
Fix pull_request trigger to target master and working branches
Fix gcovr version and update CLI flags for code coverage
Fix gcovr compatibility by using --xml output format
Implement automated regression benchmarks for synthetic geometries
Added a logo image to the README file.
Removed active development notice and original archive link.
Expanded acknowledgements section to include additional funding sources and HPC facilities used in the project.
Implement semantic layering for AI context retention and documentation
Add CI-driven Doxygen documentation generation and deployment
Add integration tests for zero and partial coverage files
@jameslehoux jameslehoux merged commit 8908190 into working Mar 7, 2026
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github-actions bot commented Mar 7, 2026

Code Coverage Report

------------------------------------------------------------------------------
                           GCC Code Coverage Report
Directory: .
------------------------------------------------------------------------------
File                                       Lines    Exec  Cover   Missing
------------------------------------------------------------------------------
src/io/CathodeWrite.H                          1       1   100%   
src/io/CathodeWrite.cpp                       95      83    87%   40-41,97-100,115-116,182-185
src/io/DatReader.H                             1       1   100%   
src/io/DatReader.cpp                         133     105    78%   26-27,30,35,92-93,99-100,107-109,135-136,141,144-147,152-155,162,164,208-209,242,245
src/io/HDF5Reader.H                            3       3   100%   
src/io/HDF5Reader.cpp                        181      85    47%   40-41,43-44,46-49,52,54-56,58-59,62,64-65,68-71,73,92-93,126-128,144-145,154-157,174-180,182-186,204,213-215,217,219-225,227,230-233,236-238,240-243,245-251,253-255,257,274,276,278,280,282,288,290,357-358,432-435,437-439
src/io/RawReader.H                             1       1   100%   
src/io/RawReader.cpp                         265     116    43%   49-50,89-90,111-112,115-117,120-121,140-142,155-157,166-168,174-177,185-186,192-196,200-204,209-212,219-223,231-237,259,263-264,270-271,273-274,276,283-284,301,312,314,318,325,327,331-334,338,346-347,353-355,361-363,365-366,369,372,374,377-380,382-384,386,388-389,391,393-394,396,398-399,401,403-404,406,410-411,413,417-418,420,425,457,463-465,471-472,521-524,526,528-530,532,534-536,538,540-542,544,546-548,550,554-556,558,562-564,566,588
src/io/TiffReader.H                            5       5   100%   
src/io/TiffReader.cpp                        378     130    34%   59-65,67-69,71-73,75-77,79-80,82-84,86-88,90-92,94-96,98-99,101-103,106-108,111-112,114-117,119,122,124-126,143-144,148-150,152-158,186,210,217,226,228-231,240,242-244,248,255,288-293,306,309-317,319-320,323-327,331-335,338-342,344-348,351-357,359-361,363,369,375-377,379-393,396,398-402,404-409,413-418,420-425,428-429,432-433,555-575,577-578,581-588,590,593-609,612-614,670,673-674,677-683,685,689-700,702-703
src/props/Diffusion.cpp                      642       0     0%   49-68,71,78-80,90,92-93,97-99,104,115-119,121-124,126-127,129-132,134-135,138-143,145-148,151-155,158,161-163,167-172,176,181-184,190-192,194,196-208,210-216,219-232,234-241,245-249,253-254,256-258,262,264-265,269-271,273-275,278-279,282-284,289-294,297,300-304,307-309,311-314,316,322-323,325-335,337,339-349,351,353-363,365-367,371,373,375-377,379-380,388-393,397-410,414-415,418-423,425,427-430,435-437,440,442-444,447,449,451,453-460,462-464,470-476,478-479,481-485,490,492-500,503-504,506-507,509,512-515,517,520,522-526,528-531,533-534,540-542,544-552,554,556-561,564-566,568,571,573-575,577-580,582-587,589-592,594,596,598-602,606,608-609,612-614,619,622-624,626,628,630,632,634,636,638-640,642,644-646,648,650,653,657-666,668-682,687-690,692,694,696,703-706,708,712,714-720,723-724,727-728,731-733,737-738,743-746,748-751,753-755,757-758,761,763,765,767-773,776-778,780,782,784,786-790,792-804,808,810,812,819-822,824,828-836,838,840-852,854,858-861,864,872-874,879-880,884-886,889-893,898-900,902-904,907-909,913-919,922-925,927-935,939,945-951,958-959,966,968-970,972-973,984,986-989,991-992,994-1002,1008,1011-1012,1015-1016,1018-1024,1027,1029-1030,1034-1038,1040-1044,1046-1047,1051-1053,1055-1056,1064,1070-1071,1073-1075,1077-1079
src/props/EffDiffFillMtx.F90                 106      91    85%   91,228-230,232-235,239-244,252
src/props/EffectiveDiffusivityHypre.cpp      480     414    86%   222-224,226-230,327,389-392,423-426,436-437,449-457,459-460,463-466,673-676,678-680,682-685,730,740,743-744,750-751,764,770-773,780,813,825-828,830-832,834
src/props/PercolationCheck.H                   4       4   100%   
src/props/PercolationCheck.cpp               125     115    92%   39-40,112-113,134-136,151,155,270
src/props/PhysicsConfig.H                     90      89    98%   150
src/props/ResultsJSON.H                      139     137    98%   230,251
src/props/Tortuosity.H                         2       2   100%   
src/props/TortuosityDirect.H                   5       5   100%   
src/props/TortuosityDirect.cpp               218     190    87%   81-83,86,100-106,113-114,125,134,140,202-209,226,436,466,475
src/props/TortuosityHypre.H                   16      16   100%   
src/props/TortuosityHypre.cpp                827     659    79%   247-250,253-255,306-307,314,322,333,339,348,372-374,377-378,380,390-392,395-397,580-583,624-627,793,858,865,867,875-876,889,893-894,896-899,901,918-920,924-925,930-936,938-942,945,958,964-967,969-971,980-983,985-987,1003,1006-1007,1030-1035,1046-1049,1051,1088,1093-1096,1099-1101,1105-1108,1110,1112-1115,1117,1122-1124,1126,1216-1219,1232-1236,1241-1246,1256-1260,1265-1270,1275-1279,1282-1285,1292-1295,1306,1315,1321,1382-1383,1457-1459,1604-1607
src/props/TortuosityHypreFill.F90            155     119    76%   97,199-204,255,263,271,277,285,287,289-292,295-298,300,303,306-318
src/props/Tortuosity_filcc.F90               122       0     0%   37,59-60,63-65,69-73,75,81,88,107,110-112,115,119-120,122,125-126,128,131-132,134,137-138,140,143-144,146,149-150,152,156-160,165-167,169,177,183,205-207,210,213-216,218-221,227-230,232-235,244-247,249-252,258-261,263-266,276-279,281-284,290-293,295-298,308,315,342-344,347-349,351-352,354,358,360-363,365-368,371,373
src/props/Tortuosity_poisson_3d.F90           66      47    71%   61,76,91,202-205,209-212,218-221,225-228
src/props/VolumeFraction.H                     4       4   100%   
src/props/VolumeFraction.cpp                  20      20   100%   
------------------------------------------------------------------------------
TOTAL                                       4084    2442    59%
------------------------------------------------------------------------------


Generated by CI — coverage data from gcovr

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codecov bot commented Mar 7, 2026

Codecov Report

✅ All modified and coverable lines are covered by tests.

📢 Thoughts on this report? Let us know!

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