workflow fix and readme edit

Author: vr1087

.github/workflows/cpp_standalone.yml

@@ -37,4 +37,4 @@ jobs:
         run: cmake --build build -j4
 
       - name: run
-        run: ./build/aligncount --help
+        run: ./build/aligncount_cpp --help

Dockerfile

@@ -67,8 +67,8 @@ RUN pip3 install pytest
 RUN pytest -q /app/tests/python/test_cli.py
 
 # 4) Verify the binaries are on PATH (just a check; you can remove)
-RUN which Aligncount && which aligncount_wrapper
+RUN which aligncount_cpp && which aligncount
 
 # Final entrypoint: run the Python wrapper by default
-ENTRYPOINT ["aligncount_wrapper"]
+ENTRYPOINT ["aligncount"]
 CMD ["--help"]

README.md

@@ -20,6 +20,8 @@ Template Repo Combines:
   - Remember to rename the `include/aligncount` directory to use your project's lowercase name and update all relevant `#include`s accordingly.
   - Replace instances of ALIGNCOUNT_VERSION with `[YOUR_PROJECT_NAME]_VERSION`
   - Set the name of the C++ executable (e.g. aligncount_cpp) to your liking in `cpp/standalone/CMakeLists.txt`
+  - Set the expected name of the C++ executable in the `cpp_standalone.yml` workflow.
+  - Set the expected name of the C++ executable and python wrapper in `DockerFile`.
 - Replace the source files with your own
 - Set GitHub action secrets for:
   - ANACONDA_TOKEN