4 consider moving data files into header files by nbassler · Pull Request #89 · APTG/libdedx

nbassler · 2026-04-01T11:21:28Z

No description provided.

…it. Checked results against tabulated values from ICRU49 and ICRU90, updated tests.

…ta references

codecov · 2026-04-01T11:22:34Z

Codecov Report

❌ Patch coverage is 70.67568% with 217 lines in your changes missing coverage. Please review.
✅ Project coverage is 72.33%. Comparing base (dd367e7) to head (4718ad1).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
examples/dedx_bench_lookup.c	0.00%	78 Missing ⚠️
tests/test_interpolation.c	62.96%	44 Missing and 26 partials ⚠️
tests/test_core_api.c	30.30%	12 Missing and 11 partials ⚠️
src/dedx.c	60.00%	16 Missing ⚠️
src/dedx_data_access.c	84.61%	10 Missing ⚠️
src/dedx_embedded_data.c	94.95%	6 Missing ⚠️
src/dedx_embedded_metadata.c	90.32%	6 Missing ⚠️
tests/test_tools.c	0.00%	3 Missing and 1 partial ⚠️
src/dedx_spline.c	96.84%	3 Missing ⚠️
src/dedx_mstar.c	75.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #89      +/-   ##
==========================================
- Coverage   73.98%   72.33%   -1.66%     
==========================================
  Files          37       38       +1     
  Lines        2856     3148     +292     
  Branches      387      452      +65     
==========================================
+ Hits         2113     2277     +164     
- Misses        693      784      +91     
- Partials       50       87      +37

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Pull request overview

This PR migrates libdedx from runtime file-based table loading to compile-time embedded datasets (generated C headers), while also introducing configurable interpolation modes for stopping-power splines and updating tests/build plumbing accordingly.

Changes:

Replace file I/O data loading with embedded table/metadata access (dedx_data_access.*, src/data/embedded/*), and remove legacy data-path/binary-table build steps.
Add interpolation-mode support (log-log vs linear) including validation and updated spline coefficient/evaluation logic.
Update CMake, CI, tests, and examples to match the new embedded-data layout and updated numeric expectations.

Reviewed changes

Copilot reviewed 109 out of 177 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
Windows/libdedx.dll	Binary artifact included/updated in PR.
Windows/dedx_ws.h	Removed legacy Windows header.
Windows/dedx_tools.h	Removed legacy Windows header.
Windows/data/short_names	Removed legacy Windows data file.
Windows/data/pstarEng.bin	Binary data artifact included/updated in PR.
Windows/data/PSTAR.bin	Binary data artifact included/updated in PR.
Windows/data/mstarEng.bin	Binary data artifact included/updated in PR.
Windows/data/MSTAR.bin	Binary data artifact included/updated in PR.
Windows/data/mstar_gas_states.dat	Removed legacy Windows metadata file.
Windows/data/icru73Eng.bin	Binary data artifact included/updated in PR.
Windows/data/ICRU73.bin	Binary data artifact included/updated in PR.
Windows/data/icru73_newEng.bin	Binary data artifact included/updated in PR.
Windows/data/ICRU73_NEW.bin	Binary data artifact included/updated in PR.
Windows/data/icru_pstarEng.bin	Binary data artifact included/updated in PR.
Windows/data/ICRU_PSTAR.bin	Binary data artifact included/updated in PR.
Windows/data/icru_astarEng.bin	Binary data artifact included/updated in PR.
Windows/data/ICRU_ASTAR.bin	Binary data artifact included/updated in PR.
Windows/data/astarEng.bin	Binary data artifact included/updated in PR.
Windows/data/ASTAR.bin	Binary data artifact included/updated in PR.
tests/test_icru90.c	New regression test asserting ICRU90 carbon data usage where available.
tests/test_icru.c	Updated expected ICRU stopping-power values to match embedded data/interpolation.
tests/test_error_codes.c	Adds config-validation test for invalid interpolation mode error.
tests/test_core_api.c	Adds min/max energy checks for ICRU carbon ranges.
tests/install_smoke_test.cmake	Removes install-smoke configuration forcing installed data path (no longer needed).
tests/CMakeLists.txt	Adds `${PROJECT_SOURCE_DIR}/src` include path for tests using internal headers.
src/dedx_validate.h	New internal validation API header split out for tests/internal usage.
src/dedx_validate.c	Switches to embedded data access and adds interpolation-mode validation.
src/dedx_tools.c	Switches to embedded data access include.
src/dedx_stopping_data.h	New internal struct describing one stopping-power table row.
src/dedx_spline.h	New spline API header (now supports log-log vs linear interpolation).
src/dedx_spline.c	New spline implementation with log-log support and linear fallback.
src/dedx_spline_base.h	Renames spline struct and adds cached `log_*` fields.
src/dedx_periodic_table.h	New periodic-table header (atomic masses/nucleons).
src/dedx_periodic_table.c	New periodic-table implementation.
src/dedx_mstar.h	New internal MSTAR helpers header.
src/dedx_mstar.c	Switches to embedded data access include.
src/dedx_mpaul.h	Switches to embedded data access include.
src/dedx_lookup_data.h	Renames internal lookup type and adds stored interpolation mode.
src/dedx_lookup_accelerator.h	Renames lookup accelerator struct to internal naming scheme.
src/dedx_embedded_metadata.h	New API for reading embedded metadata (density, gas state, I-values, composition).
src/dedx_embedded_metadata.c	Implements embedded metadata lookups from generated headers.
src/dedx_embedded_data.h	New API describing embedded program datasets and table lookup helpers.
src/dedx_data_access.h	Renames file-access API to embedded data-access API (docs updated).
src/dedx_data_access.c	Implements data access from embedded tables/metadata.
src/dedx_const.h	New internal constants header for legacy physics constants.
src/dedx_bethe.h	Updates Bethe API to use renamed internal workspace type.
src/dedx_bethe.c	Renames internal Bethe structs/types and updates allocations.
src/dedx_bethe_struct.h	Renames Bethe model/gold/workspace struct types.
src/data/embedded/dedx_icru90_pos.h	Adds generated embedded ICRU90 positron tables.
src/data/embedded/dedx_icru90_p.h	Adds generated embedded ICRU90 proton tables.
src/data/embedded/dedx_icru90_e.h	Adds generated embedded ICRU90 electron tables.
src/data/embedded/dedx_icru90_C.h	Adds generated embedded ICRU90 carbon tables.
src/data/embedded/dedx_icru90_a.h	Adds generated embedded ICRU90 alpha tables.
src/data/embedded/dedx_composition.h	Reworks embedded composition header with include guards and renamed symbols.
src/data/embedded/dedx_bethe.h	Adds generated embedded Bethe energy grid header.
src/CMakeLists.txt	Switches build to `src/` target layout, embedded data objects, and installs headers from `include/`.
python/tests/conftest.py	Adds build output candidate path under `build/src/` for the shared library.
libdedx/tools/dedx_math.h	Removes legacy math helpers header.
libdedx/tools/dedx_math.c	Removes legacy math helpers implementation.
libdedx/dedx_split.h	Removes legacy token-splitting helper header.
libdedx/dedx_split.c	Removes legacy token-splitting helper implementation.
libdedx/dedx_spline.h	Removes legacy spline header (replaced by `src/dedx_spline.h`).
libdedx/dedx_spline.c	Removes legacy spline implementation (replaced by `src/dedx_spline.c`).
libdedx/dedx_file.h	Removes legacy file-name mapping header.
libdedx/dedx_file.c	Removes legacy file-name mapping implementation.
libdedx/dedx_config.h.in	Removes configured data-path header template (no longer used).
libdedx/data/short_names	Removes legacy data file.
libdedx/data/pstarEng.dat	Removes legacy raw energy grid file.
libdedx/data/mstarEng.dat	Removes legacy raw energy grid file.
libdedx/data/icru73Eng.dat	Removes legacy raw energy grid file.
libdedx/data/icru73_newEng.dat	Removes legacy raw energy grid file.
libdedx/data/icru_pstarEng.dat	Removes legacy raw energy grid file.
libdedx/data/icru_astarEng.dat	Removes legacy raw energy grid file.
libdedx/data/estarEng.dat	Removes legacy raw energy grid file.
libdedx/data/effective_charge.dat	Removes legacy metadata file (replaced by embedded metadata).
libdedx/data/dedx_bethe.h	Removes legacy generated Bethe header.
libdedx/data/dat2c.py	Removes legacy generator script from old location.
libdedx/data/betheEng.dat	Removes legacy raw energy grid file.
libdedx/data/astarEng.dat	Removes legacy raw energy grid file.
include/dedx.h	Adds interpolation modes, updates workspace internal type forward decl, adds config field.
include/dedx_wrappers.h	New installed wrappers header under `include/`.
include/dedx_tools.h	New installed tools header under `include/`.
include/dedx_error.h	Updates error-code docs and adds invalid interpolation mode error.
examples/scripting/makefile	Removes legacy scripting example build file.
examples/scripting/main.c	Removes legacy scripting example source.
examples/scripting/libConf	Removes legacy scripting example input file.
examples/scripting/invoke_func.h	Removes legacy scripting helper header.
examples/dedx2trip/README	Removes legacy TRiP conversion example docs.
examples/dedx2trip/range.h	Removes legacy TRiP conversion helper header.
examples/dedx2trip/range.c	Removes legacy TRiP conversion helper source.
examples/dedx2trip/makefile	Removes legacy TRiP conversion makefile.
examples/dedx2trip/dedx2trip_new.h	Removes legacy TRiP conversion header.
examples/dedx2trip/dedx2trip_new.c	Removes legacy TRiP conversion source.
examples/dedx2trip/adapt.h	Removes legacy adapt integration header.
examples/dedx2trip/adapt.c	Removes legacy adapt integration source.
examples/dedx_bench_lookup.c	Adds a benchmark example comparing lookup performance across interpolation modes.
examples/CMakeLists.txt	Builds/links the new benchmark example; removes old data-copy prebuild step.
docs/doxygen/Doxyfile	Points Doxygen input to new installed headers under `include/`.
data/README.md	Documents new data layout, regeneration flow, and energy conventions.
data/raw/pstarEng.dat	Adds raw regeneration input file (currently CRLF line endings).
data/raw/mstarEng.dat	Adds raw regeneration input file (mixed CRLF/LF line endings).
data/raw/icru90_posEng.dat	Adds raw ICRU90 positron energy grid input.
data/raw/ICRU90_pos.dat	Adds raw ICRU90 positron stopping data input.
data/raw/icru90_pEng.dat	Adds raw ICRU90 proton energy grid input.
data/raw/ICRU90_p.dat	Adds raw ICRU90 proton stopping data input.
data/raw/icru90_eEng.dat	Adds raw ICRU90 electron energy grid input.
data/raw/ICRU90_e.dat	Adds raw ICRU90 electron stopping data input.
data/raw/icru90_CEng.dat	Adds raw ICRU90 carbon energy grid input.
data/raw/ICRU90_C.dat	Adds raw ICRU90 carbon stopping data input.
data/raw/icru90_aEng.dat	Adds raw ICRU90 alpha energy grid input.
data/raw/ICRU90_a.dat	Adds raw ICRU90 alpha stopping data input.
data/raw/icru73Eng.dat	Adds raw ICRU73 energy grid input (new location).
data/raw/icru73_newEng.dat	Adds raw ICRU73_NEW energy grid input (new location).
data/raw/icru_pstarEng.dat	Adds raw ICRU_PSTAR energy grid input (new location).
data/raw/icru_astarEng.dat	Adds raw ICRU_ASTAR energy grid input (new location).
data/raw/gas_states.dat	Adds raw gas-state metadata input (new location).
data/raw/estarEng.dat	Adds raw ESTAR energy grid input (new location).
data/raw/effective_charge.dat	Adds raw effective-charge metadata input (new location).
data/raw/betheEng.dat	Adds raw Bethe energy grid input (new location).
data/raw/astarEng.dat	Adds raw ASTAR energy grid input (new location).
CONTRIBUTING.md	Updates internal type naming example and removes outdated thread-safety note about file-path cache.
CMakeLists.txt	Removes data-path configuration and binary-table build; switches build to `src/`.
buildbins/dedx_build_bin.c	Removes binary table build tool source.
buildbins/CMakeLists.txt	Removes binary table build tool CMake.
.vscode/settings.json	Updates Python test configuration (currently points pytest at a likely-wrong path).
.github/workflows/ci.yml	Updates Python test env var to new build output location (`build/src/libdedx.so`).

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nbassler added 9 commits April 1, 2026 10:00

fix #88

a4aac8d

update data tables to replace binary database

9b2b480

add icru90 data

176c3a9

switch to embedded headers. Added ICRU90, updated ICRU target to use …

0d5e96e

…it. Checked results against tabulated values from ICRU49 and ICRU90, updated tests.

remove old binary handler

ea27f19

embed metadata and cleanup old code

7d68694

refactor: replace file access with data access and update embedded da…

b6a907b

…ta references

new intermediate directory structure

55aab66

move to new dir structure

fa2cdd5

Copilot AI review requested due to automatic review settings April 1, 2026 11:21

This was linked to issues Apr 1, 2026

consider moving data files into header files #4

Closed

Add ICRU 90 stopping power tables #35

Closed

linear vs log interpolation #88

Closed

github-code-quality Bot found potential problems Apr 1, 2026

View reviewed changes

Comment thread tools/dat2c.py Fixed

Copilot started reviewing on behalf of nbassler April 1, 2026 11:22 View session

nbassler and others added 3 commits April 1, 2026 13:25

clang-format fixes

7cee709

Potential fix for pull request finding 'Unused global variable'

405922c

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clang-format

dec7753

Copilot AI reviewed Apr 1, 2026

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nbassler added 3 commits April 1, 2026 13:48

fix copilot

c816275

fix clang-tidy

2a14965

Add benchmark lookup example to CI workflow for Linux and Windows

4718ad1

nbassler merged commit c62da12 into main Apr 1, 2026
22 checks passed

nbassler deleted the 4-consider-moving-data-files-into-header-files branch April 1, 2026 11:55

nbassler mentioned this pull request Apr 1, 2026

Agreement between code and the inherited should be better than 0.1 promille [TBC] #22

Closed

This was linked to issues Apr 1, 2026

Agreement between code and the inherited should be better than 0.1 promille [TBC] #22

Closed

A clearer error message #18

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4 consider moving data files into header files#89

4 consider moving data files into header files#89
nbassler merged 15 commits into
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Pull request overview

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