readme edits and workflow renames

Author: vr1087

.github/workflows/documentation.yml .github/workflows/cpp_documentation.yml.github/workflows/documentation.yml renamed to .github/workflows/cpp_documentation.yml

@@ -1,161 +1,126 @@
 # C++/Python Tool Template
 
-A reusable template for building a C++ commandline tool with a Python CLI wrapper, complete with GitHub Actions for CI, 
-Docker release, and Conda release. This template lets you jump straight into implementing a C++ tool without setting 
-up all the build, test, container, and packaging boilerplate code from scratch.
+A reusable template for building a C++ commandline tool (using HTSlib) with a Python CLI wrapper, complete with GitHub 
+Actions for CI, Docker release, and Conda release. This template lets you jump straight into implementing a C++ tool 
+without setting up all the build, test, container, and packaging boilerplate code from scratch.
 
 Template Repo Combines:
-- A **C++ executable** (`linecount` - compiled with CMake)
+- A **C++ executable** (`aligncount_cpp` - compiled with CMake)
 - A **Python wrapper** (`aligncount` - installed via pip)
 - Built-in **unit tests** (C++ and Python)
 - A **multi-stage Dockerfile** (builds, tests, and packages a wheel)
 - A **Conda recipe** (creates a cross-platform packages for Linux/macOS)
-- GitHub Actions for CI, Docker release, and Conda release
+- GitHub Actions for CI, Docker/Conda release, styling, and documentation
 
 
-## [TODO] How To
+## [TODO] How to use this template
 
 ---
-
-## Repository Layout
-
-    ├── CMakeLists.txt
-    ├──.github
-    │   └── workflows
-    │       ├── ci.yml
-    │       ├── conda_release.yml
-    │       └── docker_release.yml
-    ├── setup.py
-    ├── setup.cfg
-    ├── pyproject.toml
-    ├── src/
-    │   └── main.cpp              ← C++ “linecount” implementation
-    ├── cli/
-    │   ├── __init__.py
-    │   └── entrypoint.py         ← Python wrapper (“aligncount” console script)
-    ├── tests/
-    │   ├── cpp/
-    │   │   └── test_main.cpp     ← C++ unit test (Doctest + CTest)
-    │   └── python/
-    │       └── test_wrapper.py   ← Python unit test for format_output()
-    ├── Dockerfile                ← Multi-stage Docker build + test
-    └── .gitignore
-
----
-
-## C++ Executable (linecount)
-
-- Source: src/main.cpp
-- Build system: CMake (CMakeLists.txt)
-- Functionality: Counts non-header lines (simulates an “alignment counter”)
-- Unit test: tests/cpp/test_main.cpp using Doctest; run via CTest
-
-To build manually while at repo root:
-
-    mkdir build
-    cd build
-    cmake .. -DCMAKE_BUILD_TYPE=Release
-    cmake --build . --parallel $(nproc)
-    # Now ./linecount is available in build/
-    ./linecount sample.sam
-
----
-
-## Python Wrapper (aligncount)
-
+## Tool Descriptions
+### Python Wrapper (aligncount)
 - Source: cli/entrypoint.py
 - Entry point: aligncount console script (configured in setup.py)
-- Logic:
-  1. Parses subcommands (count-mapped or count-unmapped)
-  2. Checks that the input SAM file exists and is non-empty
-  3. Calls `linecount <path>` and formats output via format_output(cmd, raw_bytes)
-
+- Functionality:
+  - Parses subcommands (count-mapped or count-unmapped)
+  - Checks that the input SAM file exists and is non-empty
+  - Calls `aligncount_cpp -a <path>` and writes to count stdout
+### C++ Executable (aligncount_cpp)
+- Source: cpp/standalone/source/main.cpp
+- Build system: CMake (CMakeLists.txt)
+- Functionality: Counts the number of SAM records
+---
+## Installation
+### Build and install the Python Wrapper and the C++ tool
 To install in a virtualenv while at repo root:
 
     python3 -m venv venv
     source venv/bin/activate
-    pip install --upgrade pip setuptools scikit-build pytest
+    pip install --upgrade pip setuptools scikit-build
     pip install .
-    # Now you have:
-    #   - linecount  (C++ binary, in venv/bin)
-    #   - aligncount (Python wrapper, in venv/bin)
-
-Run the wrapper (just counts file lines that don't start with `@`):
 
-    aligncount count-mapped -i sample.sam
-    aligncount count-unmapped -i sample.sam
+Now you have:
+   - aligncount_cpp  (C++ binary, in venv/bin)
+   - aligncount      (Python wrapper, in venv/bin)
 
----
-
-## Unit Tests
+Run the wrapper (counts the number of SAM records in a file):
 
-### C++ Tests
-
-- Framework: Doctest (fetched via ExternalProject_Add in CMake)
-- Test file: tests/cpp/test_main.cpp
-- Run:
-
-    cd build
-    ctest --output-on-failure
+    aligncount count-mapped -a sample.sam
+    aligncount count-unmapped -a sample.sam
 
-### Python Tests
-
-- Framework: pytest
-- Test file: tests/python/test_wrapper.py
-- Run:
-
-    source venv/bin/activate
-    pytest -q
-
----
-
-## Dockerfile
+Note, the installation command implicitly builds the C++ tool via scikit-build/cmake. If you want to 
+install the Python Wrapper by itself do (does not install aligncount_cpp):
+    
+    python3 -m venv venv
+    pip install --upgrade pip setuptools
+    cd cli
+    pip install .
 
+### Dockerfile
 A multi-stage Dockerfile builds and tests everything, then produces a minimal runtime image:
-
-1. Builder stage (ubuntu:22.04):
+1. Builder stage:
    - Installs build-time dependencies (CMake, Git, Python dev headers, pip)
-   - Compiles C++ (linecount) and runs CTest
-   - Builds a Python wheel (bundles linecount + aligncount)
-
-2. Final stage (ubuntu:22.04):
+   - Compiles C++ (aligncount_cpp) and runs CTest
+   - Builds a Python wheel (bundles aligncount_cpp + aligncount)
+2. Final stage:
    - Installs runtime dependencies (Python, pip)
-   - Installs the wheel (placing linecount and aligncount into /usr/local/bin)
-   - Runs the Python unit test (pytest test_wrapper.py)
+   - Installs the wheel (placing aligncount_cpp and aligncount into /usr/local/bin)
+   - Runs the Python wrapper unit tests
    - Sets ENTRYPOINT ["aligncount"]
 
 Build and test in one command:
 
-    docker build -t your-org/aligncount-demo:latest .
+    docker build -t aligncount:latest .
 
 Run:
 
-    docker run --rm your-org/aligncount-demo:latest --help
+    docker run --rm aligncount:latest --help
 
----
 
-## Conda-Build Recipe
+### Manually build the C++ tool aligncount_cpp
+To build manually while at repo root:
 
-The `conda-recipe/meta.yaml` contains instructions for the conda-build command to create the conda package for different 
-platforms, skipping windows. The recipe expects certain environment variables to be set, which are set by the GitHub 
-action `conda_release.yml`. The expected environment variables are:
+    mkdir build
+    cd build
+    cmake ../cpp/standalone -DCMAKE_BUILD_TYPE=Release
+    cmake --build .
 
-```
-REPO_NAME   # Name of the repo, e.g. cpp-python-tool-template
-VERSION     # Tool version, e.g. 0.0.1
-TAR_URL     # URL to the repo archive, e.g. https://github.com/user/foo/archive/refs/tags/v0.0.1.tar.gz
-SHA256      # SHA256 checksum of the repo archive
-REPO_HOME   # URL to the repo home, e.g. https://github.com/user/foo
-```
+Now you have aligncount_cpp available in the build folder. Run the tool to counts SAM records:
+
+    ./aligncount -a sample.sam
 
 ---
+## Unit Tests
 
-## GitHub Actions
+### C++ Tests
+To run the C++ tool tests at repo root do:
+
+    cmake -S cpp/test -B build/test
+    cmake --build build/test
+    CTEST_OUTPUT_ON_FAILURE=1 cmake --build build/test --target test
+
+### Python Tests
+To run the python wrapper tests at repo root do:
 
-### .github/workflows/ci.yml
+    export PYTHONPATH="$PWD/cli:${PYTHONPATH}"
+    pytest tests
 
-This workflow is triggered whenever something is commited to the main branch. It builds the tool and runs the unit tests.
+The export command is required if the wrapper is not installed.
 
+---
+## GitHub Action Workflows
+
+### On new tag releases:
+- `.github/workflows/conda_release.yml` Creates and publishes a conda package for various platforms.
+- `.github/workflows/release_release.yml` Compiles and publishes the Dockerfile to docker hub.
+- `.github/workflows/cpp_documentation.yml` Builds and publishes documentation for the C++ tool.
+### On commits or pull requests to main/master branch:
+- `.github/workflows/cpp_wrapper_ci.yml` Builds, installs, and tests the C++ tool and wrapper on ubuntu.
+- `.github/workflows/cpp_install.yml` Builds, installs, and tests the C++ tool on ubuntu.
+- `.github/workflows/cpp_macos.yml` Builds and tests the C++ tool on MacOS.
+- `.github/workflows/cpp_standalone.yml` Builds the C++ tool on ubuntu.
+- `.github/workflows/cpp_ubuntu.yml` Tests the C++ tool on ubuntu.
+- `.github/workflows/cpp_style.yml` Checks C++ and CMake source style.
+---
 ### .github/workflows/docker_release.yml
 
 This workflow is triggered whenever a new tag for the repo is released. It builds the docker image for linux/amd64 
@@ -174,20 +139,26 @@ e.g. cpp-python-tool-template.
 The workflow assumes your anaconda username and token are stored as repository secrets under `ANACONDA_USER` 
 and `ANACONDA_TOKEN`.
 
-## .gitignore
+---
+## Conda-Build Recipe
 
-Included patterns to ignore:
-- macOS system files (.DS_Store, ._*)
-- CMake and CLion build directories (build/, cmake-build-debug/, _skbuild/, wheelhouse/)
-- Python venvs and caches (venv/, __pycache__/, .pytest_cache/, *.egg-info/)
-- IDE files (PyCharm/CLion .idea/, *.iml)
-- Conda build artifacts (conda-bld/, pkgs/)
+The `conda-recipe/meta.yaml` contains instructions for the conda-build command to create the conda package that 
+contains the C++ tool and the python wrapper. The recipe expects certain environment variables to be set, which 
+are set by the GitHub action `conda_release.yml`. The expected environment variables are:
 
+```
+REPO_NAME   # Name of the repo, e.g. cpp-python-tool-template
+VERSION     # Tool version, e.g. 0.0.1
+TAR_URL     # URL to the repo archive, e.g. https://github.com/user/foo/archive/refs/tags/v0.0.1.tar.gz
+SHA256      # SHA256 checksum of the repo archive
+REPO_HOME   # URL to the repo home, e.g. https://github.com/user/foo
+```
 ---
+## Miscellaneous Notes
 
+---
 ## What’s Next
 
-- Customize: Adapt this template to use the https://github.com/filipdutescu/modern-cpp-template, and include htslib
-- Write a how-to section detailing how to clone the repo and make any necessary edits
+- See github issues for this repo
 
 With this template, you have a fully tested building, packaging, and distribution pipeline out of the box. Happy coding!