two conda build outputs, renamed linecount to aligncount_cpp

Author: vr1087

CMakeLists.txt

@@ -23,16 +23,16 @@ ExternalProject_Get_Property(doctest source_dir)
 set(DOCTEST_INCLUDE_DIR ${source_dir}/doctest CACHE INTERNAL "Path to include folder for doctest")
 
 # --- Application executable ---
-add_executable(linecount src/main.cpp)
-install(TARGETS linecount RUNTIME DESTINATION bin)
+add_executable(aligncount_cpp src/main.cpp)
+install(TARGETS aligncount_cpp RUNTIME DESTINATION bin)
 
 # --- Test executable ---
 # Make test executable
-add_executable(test_linecount tests/cpp/test_main.cpp)
-target_include_directories(test_linecount PUBLIC ${DOCTEST_INCLUDE_DIR})
+add_executable(test_aligncount_cpp tests/cpp/test_main.cpp)
+target_include_directories(test_aligncount_cpp PUBLIC ${DOCTEST_INCLUDE_DIR})
 
-# Make test_linecount wait until doctest has finished downloading
-add_dependencies(test_linecount doctest)
+# Make test_aligncount_cpp wait until doctest has finished downloading
+add_dependencies(test_aligncount_cpp doctest)
 
 enable_testing()
-add_test(NAME linecount_test COMMAND test_linecount)
+add_test(NAME aligncount_cpp_test COMMAND test_aligncount_cpp)

Dockerfile

@@ -65,7 +65,7 @@ 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 linecount && which aligncount
+RUN which aligncount_cpp && which aligncount
 
 # Final entrypoint: run the Python wrapper by default
 ENTRYPOINT ["aligncount"]

cli/setup.py

@@ -0,0 +1,30 @@
+# cli/setup.py  (pure-Python installer, uses setuptools + metadata from setup_common.cfg)
+
+import os
+import configparser
+from setuptools import setup
+
+# 1) Load the same shared INI file from the parent directory
+cfg = configparser.ConfigParser()
+cfg.read(os.path.join(os.path.dirname(__file__), "..", "setup.cfg"))
+
+# 2) Extract metadata
+metadata = cfg["metadata"]
+options = cfg["options"]
+entry_points = {
+    "console_scripts": [
+        line.strip()
+        for line in cfg["options.entry_points"]["console_scripts"].splitlines()
+        if line.strip()
+    ]
+}
+
+# 3) Call setuptools.setup() with that metadata
+setup(
+    name=metadata["name"],
+    version=metadata["version"],
+    description=metadata["description"],
+    python_requires=options["python_requires"],
+    packages=["cli"],       # finds cli/__init__.py and entrypoint.py
+    entry_points=entry_points,
+)

conda-recipe/meta.yaml

@@ -1,8 +1,8 @@
-{% set REPO_NAME   = environ.get('REPO_NAME',  'cpp-python-tool-template') %}
-{% set VERSION     = environ.get('VERSION',    '0.2.37') %}
-{% set TAR_URL     = environ.get('TAR_URL',    'https://github.com/vr1087/cpp-python-tool-template/archive/refs/tags/v0.2.37.tar.gz') %}
-{% set SHA256      = environ.get('SHA256',     'c8bffc3e02bc465d0852fd124c354147a449b09e9847ff0ecaa747d083626f2a') %}
-{% set REPO_HOME   = environ.get('REPO_HOME',  'https://github.com/vr1087/cpp-python-tool-template') %}
+{% set REPO_NAME   = environ.get('REPO_NAME',  '') %}
+{% set VERSION     = environ.get('VERSION',    '') %}
+{% set TAR_URL     = environ.get('TAR_URL',    '') %}
+{% set SHA256      = environ.get('SHA256',     '') %}
+{% set REPO_HOME   = environ.get('REPO_HOME',  '') %}
 
 package:
   name: {{ REPO_NAME }}
@@ -22,22 +22,58 @@ build:
     cmake --build . --parallel ${CPU_COUNT:-1}
     cmake --install . --prefix $PREFIX
     cd ..
-    {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
   number: 0
 
 requirements:
   build:
     - {{ compiler("cxx") }}
     - cmake
-    - python
-    - pip
-    - setuptools
-    - scikit-build
   host:
-    - python
-    - scikit-build
+    # This environment only needs to run CMake and the C++ compiler
+    - {{ compiler("cxx") }}
+    - cmake
   run:
-    - python
+    # (only its C++ runtime, specified per‐output below)
+    []
+
+outputs:
+  # ---------------------------------------------------------
+  # Output #1: Arch‐specific C++ executable (aligncount-cpp)
+  # ---------------------------------------------------------
+  - name: {{ name }}_cpp
+    requirements:
+      host:
+        - {{ compiler("cxx") }}
+        - cmake
+      run:
+        - {{ cdt("libcxx") }}   # or libgcc-ng on Linux
+
+    # No separate script: top‐level build already installed
+    # the C++ binary into $PREFIX/bin/aligncount_cpp
+
+  # ---------------------------------------------------------
+  # Output #2: Noarch Python wrapper (aligncount_demo)
+  # ---------------------------------------------------------
+  - name: {{ name }}
+    noarch: python
+
+    requirements:
+      build:
+        - python >=3.9,<3.14
+        - pip
+        - setuptools
+      host:
+        - python >=3.9,<3.14
+        - pip
+        - setuptools
+      run:
+        - python >=3.9,<3.14
+        - {{ pin_subpackage(name + "_cpp", exact=True) }}
+
+    script: |
+      cd cli
+      $PYTHON -m pip install . --no-deps --ignore-installed --prefix=$PREFIX
+
 
 about:
   home: {{ REPO_HOME }}

pyproject.toml

@@ -1,15 +1,7 @@
 [build-system]
 requires = [
-    "setuptools>=42",
-    "scikit-build>=0.13",
-    "cmake>=3.18"
+    "setuptools>=46",
+    "scikit-build>=0.18",
+    "cmake>=3.5"
 ]
-build-backend = "setuptools.build_meta"
-
-[project]
-name = "aligncount_demo"
-version = "0.2.0"
-description = "Aligncount wrapper"
-
-[project.scripts]
-aligncount = "cli.entrypoint:main"
+build-backend = "setuptools.build_meta"

setup.cfg

@@ -1,15 +1,12 @@
 [metadata]
-name = aligncount_demo
-version = 0.1.0
-description = Aligncount wrapper
+name = aligncount
+version = 0.2.0
+description = Aligncount tool
 
 [options]
-# Automatically find any packages under this directory (i.e. cli/)
 packages = find:
+python_requires = >=3.9,<3.14
 
-# If you had data files, you could add:
-# include_package_data = True
-
-[options.packages.find]
-# Only look for packages under the current directory
-where = .
+[options.entry_points]
+console_scripts =
+    aligncount = cli.entrypoint:main

setup.py

@@ -1,10 +1,30 @@
-# setup.py
+# setup.py  (root, uses scikit-build + metadata from setup_common.cfg)
+
+import os
+import configparser
 from skbuild import setup
 
+# 1) Load the shared INI file
+cfg = configparser.ConfigParser()
+cfg.read(os.path.join(os.path.dirname(__file__), "setup.cfg"))
+
+# 2) Extract metadata
+metadata = cfg["metadata"]
+options = cfg["options"]
+entry_points = {
+    "console_scripts": [
+        line.strip()
+        for line in cfg["options.entry_points"]["console_scripts"].splitlines()
+        if line.strip()
+    ]
+}
+
+# 3) Call scikit-build’s setup(), passing exactly our shared metadata
 setup(
-    name="aligncount_demo",
-    version="0.2.0",
-    description="Aligncount wrapper",
-    packages=["cli"],
-    entry_points={"console_scripts": ["aligncount=cli.entrypoint:main"]},
+    name=metadata["name"],
+    version=metadata["version"],
+    description=metadata["description"],
+    python_requires=options["python_requires"],
+    packages=["cli"],       # “cli” is the only Python package at the root
+    entry_points=entry_points,
 )

tests/cpp/test_main.cpp

@@ -10,8 +10,8 @@ TEST_CASE("Count dummy SAM records") {
     f << "read2" << std::endl;
     f.close();
 
-    // run the linecount executable
-    int rc = std::system("./linecount test.sam > out.txt");
+    // run the aligncount_cpp executable
+    int rc = std::system("./aligncount_cpp test.sam > out.txt");
     CHECK(rc == 0);
 
     std::ifstream in("out.txt");