fix #74

.codecov.yml

@@ -0,0 +1,9 @@
+coverage:
+  status:
+    patch:
+      default:
+        target: 70%
+        threshold: 2%
+    project:
+      default:
+        target: auto

.github/workflows/clang-tidy.yml

@@ -24,5 +24,5 @@ jobs:
         run: |
           run-clang-tidy-19 \
             -p build \
-            -header-filter='(libdedx|tests|examples|buildbins)/' \
-            '(libdedx|tests|examples|buildbins)/.*\.c$'
+            -header-filter='(libdedx|tests|examples)/' \
+            '(libdedx|tests|examples)/.*\.c$'

CONTRIBUTING.md

@@ -2,6 +2,30 @@
 
 ## C coding style
 
+### Symbol naming and linkage
+
+Use symbol names to make visibility obvious:
+
+- Public API functions and types use the `dedx_*` prefix.
+- Shared internal helpers used across multiple `.c` files use the `dedx_internal_*` prefix.
+- File-local helpers should be declared `static` and use short unprefixed names.
+
+Examples:
+
+```c
+/* public API */
+float dedx_get_stp(dedx_workspace *ws, dedx_config *config, float energy, int *err);
+
+/* shared internal helper */
+float dedx_internal_get_atom_mass(int id, int *err);
+
+/* file-local helper */
+static int check_energy_bounds(_dedx_lookup_data *data, float energy);
+```
+
+Do not introduce new `_dedx_*` identifiers. Existing ones should be migrated to
+the scheme above as code is touched.
+
 ### Variable declarations
 
 Declare all variables at the top of their enclosing block, before any statements.
@@ -36,10 +60,12 @@ fine when the variable is genuinely local to that scope.
 ## Thread safety
 
 libdedx is currently **not thread-safe**. There is no synchronization around
-the static path cache in `_dedx_get_data_path()`, nor around workspace mutation
-in `dedx_load_config()` / `_dedx_load_data()`. Do not share a `dedx_workspace`
+the static path cache in the file-local data-path helper in
+[`libdedx/dedx_file_access.c`](libdedx/dedx_file_access.c),
+nor around workspace mutation in `dedx_load_config()` / the internal dataset
+loading helpers. Do not share a `dedx_workspace`
 across threads without external locking.
 
-The intended fix is to replace the `done` flag in `_dedx_get_data_path()` with
-C11 `call_once()`, and audit the rest of the library for shared mutable state.
-This is tracked as a known issue.
+The intended fix is to replace the cached-path `done` flag with C11
+`call_once()`, and audit the rest of the library for shared mutable state. This
+is tracked as a known issue.

README.md

@@ -1,7 +1,7 @@
 # libdedx
 
 [![CI](https://github.com/APTG/libdedx/actions/workflows/ci.yml/badge.svg)](https://github.com/APTG/libdedx/actions/workflows/ci.yml)
-[![Coverage](https://codecov.io/gh/APTG/libdedx/graph/badge.svg?branch=main)](https://codecov.io/gh/APTG/libdedx)[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
+[![Coverage](https://codecov.io/gh/APTG/libdedx/branch/main/graph/badge.svg)](https://app.codecov.io/gh/APTG/libdedx/tree/main)[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 
 A C library for stopping power calculations (dE/dx) — the energy loss of a charged particle per unit length of material.
 
@@ -20,6 +20,11 @@ Full documentation: https://aptg.github.io/libdedx/
 | `DEDX_BETHE_EXT00` | Bethe formula with extensions                 | All ions      |
 | `DEDX_ICRU`     | Auto-selects ICRU49 or ICRU73 by ion type        | p, He, heavy  |
 
+Note:
+For compound targets, `libdedx` currently extends the native coverage of some original programs by falling back to Bragg/stoichiometric weighting when the upstream database does not provide that compound directly. This applies in particular to programs such as `DEDX_PSTAR`, `DEDX_ASTAR`, and `DEDX_MSTAR`, whose original target coverage is more limited than the full set of ICRU/ESTAR-style materials exposed by `libdedx`.
+
+This behavior is useful, but it means that a result returned under a given program label is not always a direct value from the original upstream program. Future releases may separate native program coverage more explicitly from these weighted extension modes.
+
 ## Quick start
 
 One-call API for a single stopping power value:

examples/CMakeLists.txt

@@ -36,4 +36,7 @@ foreach(example dedx_example dedx_bethe dedx_list dedx_use_wrappers dedx_get_sam
     add_test(NAME ${example} COMMAND ${example})
 endforeach()
 
-install (TARGETS getdedx DESTINATION bin)
+add_test(NAME getdedx_lookup COMMAND getdedx 2 1 276 100)
+add_test(NAME getdedx_list_programs COMMAND getdedx -1 1 276 100)
+
+install (TARGETS getdedx DESTINATION bin)

examples/dedx_get.c

@@ -8,6 +8,7 @@
 
 int main(int argc, char *argv[]) {
     int err = 0;
+    int exit_code = 0;
     int prog = -1;
     int target = DEDX_WATER;
     int z = -1;
@@ -16,10 +17,17 @@ int main(int argc, char *argv[]) {
     int i = 0;
     float energy = -1.0;
     float stp = 0;
-    dedx_workspace *ws;
+    dedx_workspace *ws = NULL;
     dedx_config *cfg = (dedx_config *) calloc(1, sizeof(dedx_config));
     char *str = (char *) malloc(100);
 
+    if (cfg == NULL || str == NULL) {
+        free(cfg);
+        free(str);
+        fprintf(stderr, "Allocation failure.\n");
+        return 1;
+    }
+
     if (argc != 5) {
         dedx_get_version(&vmaj, &vmin, &vpatch);
         printf("\n This is getdedx using libdEdx version %i.%i.%i", vmaj, vmin, vpatch);
@@ -35,7 +43,7 @@ int main(int argc, char *argv[]) {
         printf("   %s MSTAR CARBON WATER 100\n", argv[0]);
         printf("   %s PSTAR HYDROGEN -1 100\n", argv[0]);
         printf("\n");
-        return 0;
+        goto cleanup;
     }
 
     if (isdigit(*argv[1]))
@@ -98,7 +106,7 @@ int main(int argc, char *argv[]) {
             i++;
         }
         printf("\n");
-        return 0;
+        goto cleanup;
     }
 
     if (z == -1) {
@@ -110,7 +118,7 @@ int main(int argc, char *argv[]) {
             i++;
         }
         printf("\n");
-        return 0;
+        goto cleanup;
     }
 
     if (target == -1) {
@@ -124,7 +132,7 @@ int main(int argc, char *argv[]) {
         printf("\nAdditional materials are possible by Braggs additivity rule,\n");
         printf("as long as the constituent elements are availble in the list above.");
         printf("\n");
-        return 0;
+        goto cleanup;
     }
 
     if (energy == -1) {
@@ -133,7 +141,7 @@ int main(int argc, char *argv[]) {
                dedx_get_ion_name(z),
                dedx_get_min_energy(prog, z),
                dedx_get_max_energy(prog, z));
-        return 0;
+        goto cleanup;
     }
 
     if ((energy < dedx_get_min_energy(prog, z)) || (energy > dedx_get_max_energy(prog, z))) {
@@ -142,7 +150,8 @@ int main(int argc, char *argv[]) {
                dedx_get_ion_name(z),
                dedx_get_min_energy(prog, z),
                dedx_get_max_energy(prog, z));
-        exit(-1);
+        exit_code = 1;
+        goto cleanup;
     }
 
     if (prog == DEDX_ESTAR) {
@@ -166,7 +175,8 @@ int main(int argc, char *argv[]) {
         fprintf(stderr, "dedx_initialize, error %i:", err);
         dedx_get_error_code(str, err);
         fprintf(stderr, "  %s\n", str);
-        exit(1);
+        exit_code = 1;
+        goto cleanup;
     }
 
     /* load configuration */
@@ -179,7 +189,8 @@ int main(int argc, char *argv[]) {
         fprintf(stderr, "dedx_load_config, error %i:", err);
         dedx_get_error_code(str, err);
         fprintf(stderr, "  %s\n", str);
-        exit(1);
+        exit_code = 1;
+        goto cleanup;
     }
 
     /* get stopping power */
@@ -188,7 +199,8 @@ int main(int argc, char *argv[]) {
         fprintf(stderr, "dedx_read_energy, error %i:", err);
         dedx_get_error_code(str, err);
         fprintf(stderr, "  %s\n", str);
-        exit(1);
+        exit_code = 1;
+        goto cleanup;
     }
 
     /* check if braggs additivity rule was used */
@@ -198,9 +210,11 @@ int main(int argc, char *argv[]) {
     }
     printf("1/rho dE/dx = %6.3E MeV cm2/g\n", stp);
 
-    dedx_free_workspace(ws, &err);
+cleanup:
+    if (ws != NULL)
+        dedx_free_workspace(ws, &err);
     dedx_free_config(cfg, &err);
     free(str);
 
-    return 0;
+    return exit_code;
 }

examples/dedx_get_sample_csv.c

@@ -1,5 +1,6 @@
 #include <dedx.h>
 #include <stdio.h>
+#include <stdlib.h>
 
 #include "dedx_wrappers.h"
 
@@ -10,6 +11,10 @@ int main() {
     const int ions[] = {DEDX_HYDROGEN, DEDX_HELIUM, DEDX_OXYGEN, DEDX_CARBON, DEDX_URANIUM, DEDX_IRON, -1};
 
     FILE *file = fopen("result.txt", "a");
+    if (file == NULL) {
+        fprintf(stderr, "Unable to open result.txt for writing.\n");
+        return 1;
+    }
     fprintf(file, "Program, Material, Ion, Energy, Stopping Power \n");
     for (int i = 0; programs[i] != -1; i++) {
         const char *prog_name = dedx_get_program_name(programs[i]);

examples/dedx_use_wrappers.c

@@ -1,5 +1,6 @@
 #include <dedx.h>
 #include <stdio.h>
+#include <stdlib.h>
 
 #include "dedx_wrappers.h"
 

libdedx/CMakeLists.txt

@@ -1,7 +1,7 @@
 # ESTAR removed from installer
-set(dedx_data data/ASTAR.bin data/astarEng.dat data/mstarEng.dat data/pstarEng.bin data/ASTAR.dat data/compos.txt data/MSTAR.dat data/gas_states.dat data/pstarEng.dat data/astarEng.bin data/effective_charge.dat data/MSTAR.bin data/mstarEng.bin data/PSTAR.bin data/PSTAR.dat data/short_names data/ICRU73.dat data/ICRU73.bin data/ICRU_PSTAR.dat data/ICRU_PSTAR.bin data/ICRU_ASTAR.dat data/ICRU_ASTAR.bin data/icru73Eng.dat data/icru73Eng.bin data/ICRU73_NEW.dat data/ICRU73_NEW.bin data/icru73_newEng.dat data/icru73_newEng.bin data/composition data/betheEng.dat data/betheEng.bin data/icru_pstarEng.dat data/icru_pstarEng.bin data/icru_astarEng.dat data/icru_astarEng.bin data/atima_compos)
+set(dedx_data data/ASTAR.bin data/astarEng.dat data/mstarEng.dat data/pstarEng.bin data/ASTAR.dat data/compos.txt data/MSTAR.dat data/gas_states.dat data/pstarEng.dat data/astarEng.bin data/effective_charge.dat data/MSTAR.bin data/mstarEng.bin data/PSTAR.bin data/PSTAR.dat data/short_names data/ICRU73.dat data/ICRU73.bin data/ICRU_PSTAR.dat data/ICRU_PSTAR.bin data/ICRU_ASTAR.dat data/ICRU_ASTAR.bin data/icru73Eng.dat data/icru73Eng.bin data/ICRU73_NEW.dat data/ICRU73_NEW.bin data/icru73_newEng.dat data/icru73_newEng.bin data/composition data/betheEng.dat data/betheEng.bin data/icru_pstarEng.dat data/icru_pstarEng.bin data/icru_astarEng.dat data/icru_astarEng.bin)
 
-set(dedx_data_bin data/ASTAR.bin data/astarEng.bin data/ICRU73.bin data/icru73Eng.bin data/ICRU73_NEW.bin data/icru73_newEng.bin data/MSTAR.bin data/mstarEng.bin data/PSTAR.bin data/ICRU_PSTAR.bin data/ICRU_ASTAR.bin data/pstarEng.bin data/betheEng.bin data/icru_astarEng.bin data/icru_pstarEng.bin data/compos.txt data/effective_charge.dat data/short_names data/composition data/gas_states.dat data/atima_compos)
+set(dedx_data_bin data/ASTAR.bin data/astarEng.bin data/ICRU73.bin data/icru73Eng.bin data/ICRU73_NEW.bin data/icru73_newEng.bin data/MSTAR.bin data/mstarEng.bin data/PSTAR.bin data/ICRU_PSTAR.bin data/ICRU_ASTAR.bin data/pstarEng.bin data/betheEng.bin data/icru_astarEng.bin data/icru_pstarEng.bin data/compos.txt data/effective_charge.dat data/short_names data/composition data/gas_states.dat)
 
 # Object library: compiled once with -fPIC so the objects feed both the
 # static and the shared library without a second compilation pass.
@@ -47,7 +47,7 @@ if(NOT WIN32)
     target_link_libraries(dedx_shared PUBLIC m)
 endif()
 
-install(FILES dedx.h dedx_error.h dedx_tools.h dedx_wrappers.h DESTINATION include)
+install(FILES dedx.h dedx_elements.h dedx_error.h dedx_tools.h dedx_wrappers.h DESTINATION include)
 
 install(TARGETS dedx dedx_shared
     RUNTIME DESTINATION bin