cf-streamfind 0.1.0__tar.gz

cf_streamfind-0.1.0/PKG-INFO

@@ -0,0 +1,23 @@
+Metadata-Version: 2.4
+Name: cf-streamfind
+Version: 0.1.0
+Summary: CogniFlow package with processing steps based on the StreamFind native algorithms.
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Provides-Extra: test
+Requires-Dist: pytest<9.0,>=8.0; extra == "test"
+
+# cf-streamfind
+
+Generated CogniFlow step-package scaffold.
+
+- Package id: `cf.streamfind`
+- Python module: `cf_streamfind`
+- Manifest: `src/cf_streamfind/steps.nq`
+- C++ source: `src/cf_streamfind/cpp/steps.cpp`
+
+Install locally:
+
+```bash
+pip install .
+```

cf_streamfind-0.1.0/README.md

@@ -0,0 +1,14 @@
+# cf-streamfind
+
+Generated CogniFlow step-package scaffold.
+
+- Package id: `cf.streamfind`
+- Python module: `cf_streamfind`
+- Manifest: `src/cf_streamfind/steps.nq`
+- C++ source: `src/cf_streamfind/cpp/steps.cpp`
+
+Install locally:
+
+```bash
+pip install .
+```

cf_streamfind-0.1.0/pyproject.toml

@@ -0,0 +1,28 @@
+[build-system]
+requires = ["setuptools>=70", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "cf-streamfind"
+version = "0.1.0"
+description = "CogniFlow package with processing steps based on the StreamFind native algorithms."
+readme = "README.md"
+requires-python = ">=3.10"
+dependencies = []
+
+[project.optional-dependencies]
+test = [
+	"pytest>=8.0,<9.0",
+]
+
+[project.entry-points."cogniflow.steps"]
+"cf.streamfind" = "cf_streamfind:steps.nq"
+
+[tool.setuptools]
+package-dir = {"" = "src"}
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+cf_streamfind = ["steps.nq", "cpp/*.cpp", "cpp/CMakeLists.txt"]

cf_streamfind-0.1.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

cf_streamfind-0.1.0/src/cf_streamfind/__init__.py

@@ -0,0 +1,3 @@
+"""Generated CogniFlow step package (cf.streamfind)."""
+
+__all__ = ["steps"]

cf_streamfind-0.1.0/src/cf_streamfind/cpp/CMakeLists.txt

@@ -0,0 +1,78 @@
+cmake_minimum_required(VERSION 3.20)
+project(cf_streamfind_steps LANGUAGES CXX)
+
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
+get_filename_component(_CF_REPO_ROOT "${CMAKE_CURRENT_SOURCE_DIR}/../../../../../" ABSOLUTE)
+include("${_CF_REPO_ROOT}/tools/cmake/cf_contracts_include.cmake")
+
+set(GENERATED_DIR ${CMAKE_CURRENT_BINARY_DIR}/generated)
+file(MAKE_DIRECTORY ${GENERATED_DIR})
+
+set(STEPS_DOCUMENT ${CMAKE_CURRENT_SOURCE_DIR}/../steps.nq)
+set(SIG_HEADER ${GENERATED_DIR}/cf_streamfind_signature_hashes.h)
+
+set(CF_SIGGEN_COMMAND ${Python3_EXECUTABLE} -m cf_step_tooling.siggen)
+execute_process(
+  COMMAND ${Python3_EXECUTABLE} -c
+          "import inspect, pathlib, cf_step_tooling.siggen as sig, cf_step_tooling._signatures as impl, cf_step_tooling._step_document as doc, cf_step_tooling._rdf as rdf; print(pathlib.Path(inspect.getsourcefile(sig)).resolve()); print(pathlib.Path(inspect.getsourcefile(impl)).resolve()); print(pathlib.Path(inspect.getsourcefile(doc)).resolve()); print(pathlib.Path(inspect.getsourcefile(rdf)).resolve())"
+  OUTPUT_VARIABLE CF_SIGGEN_DEPENDENCY_OUTPUT
+  OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+string(REPLACE "\r\n" "\n" CF_SIGGEN_DEPENDENCY_OUTPUT "${CF_SIGGEN_DEPENDENCY_OUTPUT}")
+string(REPLACE "\n" ";" CF_SIGGEN_DEPENDENCIES "${CF_SIGGEN_DEPENDENCY_OUTPUT}")
+
+add_custom_command(
+  OUTPUT ${SIG_HEADER}
+  COMMAND ${CF_SIGGEN_COMMAND} --steps ${STEPS_DOCUMENT} --out ${SIG_HEADER} --scratch
+  DEPENDS ${STEPS_DOCUMENT} ${CF_SIGGEN_DEPENDENCIES}
+  COMMENT "Generating cf_streamfind signature hashes"
+)
+
+find_package(ZLIB QUIET)
+if(ZLIB_FOUND)
+  set(CF_STREAMFIND_ZLIB_LIBS ZLIB::ZLIB)
+  set(CF_STREAMFIND_HAS_ZLIB TRUE)
+else()
+  find_library(ZLIB_LIBRARY z PATHS $ENV{ZLIB_ROOT}/lib)
+  find_path(ZLIB_INCLUDE_DIR zlib.h PATHS $ENV{ZLIB_ROOT}/include)
+  if(ZLIB_LIBRARY AND ZLIB_INCLUDE_DIR)
+    set(CF_STREAMFIND_ZLIB_LIBS ${ZLIB_LIBRARY})
+    set(CF_STREAMFIND_HAS_ZLIB TRUE)
+  else()
+    set(CF_STREAMFIND_HAS_ZLIB FALSE)
+    message(WARNING "zlib not found; mzML zlib decompression will not be available.")
+  endif()
+endif()
+
+add_library(${PROJECT_NAME} SHARED
+  ${CMAKE_CURRENT_SOURCE_DIR}/steps.cpp
+  ${SIG_HEADER}
+)
+
+target_include_directories(${PROJECT_NAME} PRIVATE
+  ${CF_CONTRACTS_INCLUDE}
+  ${GENERATED_DIR}
+  ${CMAKE_CURRENT_SOURCE_DIR}
+)
+
+if(CF_STREAMFIND_HAS_ZLIB)
+  target_include_directories(${PROJECT_NAME} PRIVATE ${ZLIB_INCLUDE_DIR})
+  target_link_libraries(${PROJECT_NAME} PRIVATE ${CF_STREAMFIND_ZLIB_LIBS})
+  target_compile_definitions(${PROJECT_NAME} PRIVATE CF_STREAMFIND_HAS_ZLIB=1)
+endif()
+
+target_compile_definitions(${PROJECT_NAME} PRIVATE CF_STEP_ABI_EXPORTS)
+
+add_custom_command(TARGET ${PROJECT_NAME} POST_BUILD
+  COMMAND ${CMAKE_COMMAND} -E make_directory ${CMAKE_CURRENT_SOURCE_DIR}/../bin
+  COMMAND ${CMAKE_COMMAND} -E copy $<TARGET_FILE:${PROJECT_NAME}> ${CMAKE_CURRENT_SOURCE_DIR}/../bin
+)
+
+if(DEFINED SKBUILD_PLATLIB_DIR AND NOT SKBUILD_PLATLIB_DIR STREQUAL "")
+  add_custom_command(TARGET ${PROJECT_NAME} POST_BUILD
+    COMMAND ${CMAKE_COMMAND} -E make_directory ${SKBUILD_PLATLIB_DIR}/cf_streamfind/bin
+    COMMAND ${CMAKE_COMMAND} -E copy $<TARGET_FILE:${PROJECT_NAME}> ${SKBUILD_PLATLIB_DIR}/cf_streamfind/bin
+  )
+endif()