Re-organize repository (part 3)

- address #89

- update makefiles, scripts, and continuous integration setup

(see previous commit 90b1741 "Re-organize repository (part 1)"
(see previous commit dc521a4 "Re-organize repository (part 2)"

.github/workflows/check_doc.yml

@@ -24,4 +24,4 @@ jobs:
         sudo apt-get install doxygen doxygen-latex graphviz
 
     - name: Build documentation and check for warnings
-      run: make clean doc
+      run: make clean clean_doc doc

.github/workflows/main_nix.yml

@@ -29,20 +29,20 @@ jobs:
 
     - name: Run binary
       run: |
-        make clean bin bint_run
-        make clean bin_debug_severe bint_run
+        make clean bin_run
+        make clean bin_debug_severe
 
     - name: Unit tests
-      run: make clean test test_run
+      run: make clean test_run
 
     - name: Severe unit tests (without sanitizers)
       if: ${{ runner.os == 'macOS' }}
-      run: make clean test_severe test_run
+      run: make clean test_severe
 
     - name: Severe unit tests (with sanitizers)
       # Apple clang does not support "AddressSanitizer: detect_leaks" (at least as of clang-1200.0.32.29)
       if: ${{ runner.os != 'macOS' }}
-      run: ASAN_OPTIONS=detect_leaks=1:strict_string_checks=1:detect_stack_use_after_return=1:check_initialization_order=1:strict_init_order=1 LSAN_OPTIONS=suppressions=.LSAN_suppr.txt make clean test_severe test_run
+      run: make clean test_leaks
 
 
   check_code_coverage:
@@ -55,7 +55,7 @@ jobs:
         submodules: recursive
 
     - name: Generate coverage report
-      run: make clean cov cov_run
+      run: CC=gcc CXX=g++ GCOV=gcov make clean clean_cov cov
 
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v3

.github/workflows/main_win.yml

@@ -40,7 +40,7 @@ jobs:
 
     # AddressSanitizer and LeakSanitizer not available on cygwin
     - name: Run binary
-      run: make clean bin bint_run
+      run: make clean bin_run
 
     - name: Unit tests
-      run: make clean test test_run
+      run: make clean test_run

README.md

@@ -99,7 +99,7 @@ A full code documentation may be built, see [here](#get_documentation).
       - for unit tests (using `googletest`), additionally,
         - `g++ >= v5.0` or `clang++ >= v5.0` compliant with `C++11`
         - `POSIX API`
-    - POSIX- or GNU-compliant `make`
+    - GNU-compliant `make`
     - On Windows OS: an installation of `cygwin`
 
   * Clone the repository
@@ -244,7 +244,7 @@ for one generic location
 (it is a relatively wet and cool site in the sagebrush steppe).
 
 ```{.sh}
-      make bin bint_run
+      make bin_run
 ```
 
 The simulated output is stored at `tests/example/Output/`.
@@ -262,12 +262,12 @@ The following steps provide a starting point for such comparisons:
 ```{.sh}
       # Simulate on refernce branch and copy output to "Output_ref"
       git checkout master
-      make bin bint_run
+      make bin_run
       cp -r tests/example/Output tests/example/Output_ref
 
       # Switch to development branch <branch_xxx> and run the same simulation
       git checkout <branch_xxx>
-      make bin bint_run
+      make bin_run
 
       # Compare the two sets of outputs
       #   * Lists all output files and determine if they are exactly they same
@@ -289,17 +289,17 @@ Currently, the following is implemented:
        and some slope/aspect/day of year combinations
 
 ```{.sh}
-      CPPFLAGS=-DSW2_SolarPosition_Test__hourangles_by_lat_and_doy make test test_run
+      CPPFLAGS=-DSW2_SolarPosition_Test__hourangles_by_lat_and_doy make test_run
       Rscript tools/plot__SW2_SolarPosition_Test__hourangles_by_lat_and_doy.R
 
-      CPPFLAGS=-DSW2_SolarPosition_Test__hourangles_by_lats make test test_run
+      CPPFLAGS=-DSW2_SolarPosition_Test__hourangles_by_lats make test_run
       Rscript tools/plot__SW2_SolarPosition_Test__hourangles_by_lats.R
 ```
 
   - PET plots as function of radiation, relative humidity, wind speed, and cover
 
 ```{.sh}
-      CPPFLAGS=-DSW2_PET_Test__petfunc_by_temps make test test_run
+      CPPFLAGS=-DSW2_PET_Test__petfunc_by_temps make test_run
       Rscript tools/plot__SW2_PET_Test__petfunc_by_temps.R
 ```