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Add CI-driven Doxygen documentation generation and deployment#115

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jameslehoux merged 2 commits intomasterfrom
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Mar 6, 2026
Merged

Add CI-driven Doxygen documentation generation and deployment#115
jameslehoux merged 2 commits intomasterfrom
working

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jameslehoux and others added 2 commits March 6, 2026 13:25
Three new files implement CI-driven API documentation:

1. Doxyfile — Configured for the project with:
   - SVG class hierarchy and include dependency graphs (Graphviz)
   - Collaboration diagrams showing AMReX/HYPRE interfaces
   - Directory dependency graphs
   - Tree-view navigation with search
   - All public APIs extracted from the doxygen comments
     standardized in the previous commit

2. docs/mainpage.md — Landing page with:
   - Architecture overview table (I/O, Physics, Fortran layers)
   - Cross-referenced class listing (@ref links)
   - Data flow diagram

3. .github/workflows/docs.yml — GitHub Actions workflow that:
   - Triggers on pushes to master that touch src/, docs/, or Doxyfile
   - Installs doxygen + graphviz on ubuntu-latest
   - Builds HTML documentation
   - Deploys to GitHub Pages via actions/deploy-pages@v4
   - Supports manual dispatch via workflow_dispatch

Note: GitHub Pages must be configured to use "GitHub Actions" as the
source (Settings > Pages > Source) for the deployment to work.

https://claude.ai/code/session_01R6ttf92LsJvRQayiPi8xCw
…n-setup-7bMLw

Add automated Doxygen documentation generation (#110)
@jameslehoux jameslehoux merged commit 667ee88 into master Mar 6, 2026
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github-actions bot commented Mar 6, 2026

Code Coverage Report

------------------------------------------------------------------------------
                           GCC Code Coverage Report
Directory: .
------------------------------------------------------------------------------
File                                       Lines    Exec  Cover   Missing
------------------------------------------------------------------------------
src/io/CathodeWrite.H                          1       0     0%   60
src/io/CathodeWrite.cpp                       92       0     0%   15,17-19,24,27,34-36,39-41,46,50-52,59,62,65-69,72-74,78-79,83-91,93,96-100,103-105,109-111,114-116,121,125-127,136,139-143,145-148,151-162,168-171,175,177,181-185,188-190
src/io/DatReader.H                             1       0     0%   59
src/io/DatReader.cpp                         128       0     0%   26-27,30,35,39,41,55,59-60,62-63,69-70,73-79,81-84,87-88,90-93,96-100,105,107-109,112-115,117-119,122-125,127-131,133,135-136,140-141,143-147,150-155,160,162,164,168-171,176-177,179-180,182-183,185-189,191-192,195-197,199-203,205-209,211,215,217,220-224,227,232-240,242,244-245,247,252-253
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     112    89%   39-40,112-113,134-136,141-143,151,155,270
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                   1       0     0%   80
src/props/TortuosityDirect.cpp               167       0     0%   41,47-52,54-56,59,63-64,68,70-74,78-80,82-84,86-87,90-92,94-95,97-108,112,115-116,119,121-122,125,127-129,131,134,136-137,140,142-143,150,153-155,157-159,161-165,167-171,173-176,178-181,183-189,192-194,196-197,202,204-211,216,218-220,222-223,227-228,231-232,236-238,240-241,244,274-275,279,281,283,286,349-351,357,359,362,371-373,375,379-380,384-385,388-390,394-395,398-399,402,419-421,424,445-447,449,452-456,458-459,463
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       0     0%   29-30,50-52,56-61,63,71-76,78,86-91,93,99,105-106,132,134,140-142,147,152,158,178-179,182,185-188,193-196,202-205,209-212,218-221,225-228,235,239
src/props/VolumeFraction.H                     4       4   100%   
src/props/VolumeFraction.cpp                  20      20   100%   
------------------------------------------------------------------------------
TOTAL                                       4021    2007    49%
------------------------------------------------------------------------------


Generated by CI — coverage data from gcovr

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codecov bot commented Mar 6, 2026

Codecov Report

✅ All modified and coverable lines are covered by tests.

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