pyncbitk-runtime 29.6.0.0__tar.gz

pyncbitk_runtime-29.6.0.0/CMakeLists.txt

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+cmake_minimum_required(VERSION 3.20)
+
+if(DEFINED SKBUILD_PROJECT_NAME)
+    project(${SKBUILD_PROJECT_NAME} VERSION ${SKBUILD_PROJECT_VERSION})
+else()
+    project(pyncbitk-runtime)
+endif()
+
+enable_language(C)
+enable_language(CXX)
+
+set(BUILD_SHARED_LIBS OFF)
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+
+# Detect required NCBI C++ Toolkit libraries
+#find_package(PCRE REQUIRED)
+#find_package(lzo REQUIRED)
+#find_package(libunwind REQUIRED)
+#find_package(ncbi-cxx-toolkit-public COMPONENTS algo core seqext REQUIRED)
+
+# Configure Toolkit build
+set(NCBI_WITHOUT_MT ON)
+
+# Install all dependencies into `pyncbitk-runtime` wheel
+if("${SKBUILD_STATE}" STREQUAL "wheel")
+    execute_process(
+        COMMAND conan install ${CMAKE_SOURCE_DIR} 
+            -nr --deployer deployer 
+            --deployer-folder "${SKBUILD_PLATLIB_DIR}/${SKBUILD_PROJECT_NAME}" 
+            -s compiler.cppstd=20)
+endif()

pyncbitk_runtime-29.6.0.0/COPYING

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+MIT License
+
+Copyright (c) 2024 Martin Larralde <martin.larralde@embl.de>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

pyncbitk_runtime-29.6.0.0/PKG-INFO

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+Metadata-Version: 2.2
+Name: pyncbitk-runtime
+Version: 29.6.0.0
+Summary: Runtime component of the NCBI C++ Toolkit to use in PyNCBItk.
+Keywords: bioinformatics,blast,sequence,alignment,ncbi
+Author-Email: Martin Larralde <martin.larralde@embl.de>
+License: MIT License
+         
+         Copyright (c) 2024 Martin Larralde <martin.larralde@embl.de>
+         
+         Permission is hereby granted, free of charge, to any person obtaining a copy
+         of this software and associated documentation files (the "Software"), to deal
+         in the Software without restriction, including without limitation the rights
+         to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+         copies of the Software, and to permit persons to whom the Software is
+         furnished to do so, subject to the following conditions:
+         
+         The above copyright notice and this permission notice shall be included in all
+         copies or substantial portions of the Software.
+         
+         THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+         IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+         FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+         AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+         LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+         OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+         SOFTWARE.
+         
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: C++
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Project-URL: Documentation, https://pyncbitk.readthedocs.io/en/stable/
+Project-URL: Bug Tracker, https://github.com/althonos/pyncbitk/issues
+Project-URL: Changelog, https://github.com/althonos/pyncbitk/blob/master/CHANGELOG.md
+Project-URL: Coverage, https://codecov.io/gh/althonos/pyncbitk/
+Project-URL: Builds, https://github.com/althonos/pyncbitk/actions
+Project-URL: PyPI, https://pypi.org/project/pyncbitk
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+
+# 🧬🧰 PyNCBItk [![Stars](https://img.shields.io/github/stars/althonos/pyncbitk.svg?style=social&maxAge=3600&label=Star)](https://github.com/althonos/pyncbitk/stargazers)
+
+*(Unofficial) [Cython](https://cython.org/) bindings and Python interface to the [NCBI C++ Toolkit](https://www.ncbi.nlm.nih.gov/toolkit).*
+
+This package contains the runtime components of PyNCBItk to allow reusing them
+across versions of the Cython bindings without having to rebuild. See the main
+[`pyncbitk`](https://pypi.org/project/pyncbitk) package for more information.
+
+
+## 🔧 Installing
+
+The PyNCBItk runtime supports pre-built binaries for Linux x86-64 (based on `manylinux_2_34`),
+and for MacOS x86-64 and Aarch64 (for MacOS 13.3+). At the moment, the package is only tested
+on these platforms.
+
+Compiling from scratch uses CMake and the [Conan C/C++ package manager](https://docs.conan.io/2/)
+to build the official [`ncbi-cxx-toolkit-public` recipe](https://github.com/ncbi/ncbi-cxx-toolkit-conan)
+and install the artifacts into a self-contained Python package. If compilation fails for your
+platform, please open an issue on the [issue tracker](https://github.com/althonos/pyncbitk/issues).
+
+
+## ⚖️ License
+
+This library is provided under the [MIT License](https://choosealicense.com/licenses/mit/).
+The NCBI C++ Toolkit is a "United States Government Work" and therefore lies in
+the public domain, but may be subject to copyright by the U.S. in foreign
+countries. Some restrictions apply, see the
+[NCBI C++ Toolkit license](https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/doc/public/LICENSE).

pyncbitk_runtime-29.6.0.0/README.md

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+# 🧬🧰 PyNCBItk [![Stars](https://img.shields.io/github/stars/althonos/pyncbitk.svg?style=social&maxAge=3600&label=Star)](https://github.com/althonos/pyncbitk/stargazers)
+
+*(Unofficial) [Cython](https://cython.org/) bindings and Python interface to the [NCBI C++ Toolkit](https://www.ncbi.nlm.nih.gov/toolkit).*
+
+This package contains the runtime components of PyNCBItk to allow reusing them
+across versions of the Cython bindings without having to rebuild. See the main
+[`pyncbitk`](https://pypi.org/project/pyncbitk) package for more information.
+
+
+## 🔧 Installing
+
+The PyNCBItk runtime supports pre-built binaries for Linux x86-64 (based on `manylinux_2_34`),
+and for MacOS x86-64 and Aarch64 (for MacOS 13.3+). At the moment, the package is only tested
+on these platforms.
+
+Compiling from scratch uses CMake and the [Conan C/C++ package manager](https://docs.conan.io/2/)
+to build the official [`ncbi-cxx-toolkit-public` recipe](https://github.com/ncbi/ncbi-cxx-toolkit-conan)
+and install the artifacts into a self-contained Python package. If compilation fails for your
+platform, please open an issue on the [issue tracker](https://github.com/althonos/pyncbitk/issues).
+
+
+## ⚖️ License
+
+This library is provided under the [MIT License](https://choosealicense.com/licenses/mit/).
+The NCBI C++ Toolkit is a "United States Government Work" and therefore lies in
+the public domain, but may be subject to copyright by the U.S. in foreign
+countries. Some restrictions apply, see the
+[NCBI C++ Toolkit license](https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/doc/public/LICENSE).

pyncbitk_runtime-29.6.0.0/conanfile.txt

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+[requires]
+ncbi-cxx-toolkit-public/29.6.0
+libiconv/1.17
+[options]
+ncbi-cxx-toolkit-public/*:with_components=algo;core;objects;seqext;loaders
+ncbi-cxx-toolkit-public/*:without_req=BerkeleyDB;GRPC
+ncbi-cxx-toolkit-public/*:shared=True
+[layout]
+cmake_layout
+[generators]
+CMakeDeps
+CMakeToolchain
+VirtualRunEnv

pyncbitk_runtime-29.6.0.0/deployer.py

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+import filecmp
+import os
+import glob
+import shutil
+import fnmatch
+
+from conan.internal.cache.home_paths import HomePaths
+from conan.api.output import ConanOutput
+from conan.internal.loader import load_python_file
+from conan.internal.errors import conanfile_exception_formatter
+from conan.errors import ConanException
+from conan.internal.util.files import rmdir, mkdir
+
+
+def _deploy_single(dep, conanfile, output_folder, folder_name):
+    new_folder = os.path.join(output_folder, folder_name)
+    rmdir(new_folder)
+    symlinks = conanfile.conf.get("tools.deployer:symlinks", check_type=bool, default=True)
+    try:
+        shutil.copytree(dep.package_folder, new_folder, symlinks=symlinks)
+        if os.path.exists(os.path.join(new_folder, "bin")):
+            shutil.rmtree(os.path.join(new_folder, "bin"))
+    except Exception as e:
+        if "WinError 1314" in str(e):
+            ConanOutput().error("full_deploy: Symlinks in Windows require admin privileges "
+                                "or 'Developer mode = ON'", error_type="exception")
+        raise ConanException(f"full_deploy: The copy of '{dep}' files failed: {e}.\nYou can "
+                             f"use 'tools.deployer:symlinks' conf to disable symlinks")
+    dep.set_deploy_folder(new_folder)
+
+    config_file = os.path.join(output_folder, f"{dep.ref.name}-config.cmake")
+    libfiles = glob.glob(os.path.join(new_folder, "lib", "*"))
+    libs = " ".join(
+        f"${{CMAKE_CURRENT_LIST_DIR}}/{folder_name}/lib/{os.path.basename(libfile)}"
+        for libfile in libfiles
+    )
+
+    with open(config_file, "w") as dst:
+        dst.write(f"set({dep.ref.name}_INCLUDE_DIRS ${{CMAKE_CURRENT_LIST_DIR}}/{folder_name}/include)\n")
+        dst.write(f"set({dep.ref.name}_LIBRARIES {libs})\n")
+
+
+
+
+def deploy(graph, output_folder, **kwargs):
+    conanfile = graph.root.conanfile
+    for dep in conanfile.dependencies.values():
+        if dep.package_folder is None:
+            continue
+        folder_name = dep.ref.name #os.path.join("full_deploy", dep.context, dep.ref.name, str(dep.ref.version))
+        build_type = dep.info.settings.get_safe("build_type")
+        arch = dep.info.settings.get_safe("arch")
+        #if build_type:
+        #    folder_name = os.path.join(folder_name, build_type)
+        #if arch:
+        #    folder_name = os.path.join(folder_name, arch)
+        #print("install dep:", dep)
+        _deploy_single(dep, conanfile, output_folder, folder_name)

pyncbitk_runtime-29.6.0.0/pyproject.toml

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+[build-system]
+build-backend = "scikit_build_core_conan.build"
+requires = [
+    "scikit-build-core-conan==0.7.1 ; python_version <= '3.8'", 
+    "scikit-build-core-conan>=0.8.0 ; python_version > '3.8'", 
+    "cython >=3.0"
+]
+
+[project]
+name = "pyncbitk-runtime"
+version = "29.6.0.0"
+description = "Runtime component of the NCBI C++ Toolkit to use in PyNCBItk."
+readme = "README.md"
+requires-python = ">=3.7"
+license = { file = "COPYING" }
+authors = [
+  { name = "Martin Larralde", email = "martin.larralde@embl.de" },
+]
+keywords = ["bioinformatics", "blast", "sequence", "alignment", "ncbi"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Programming Language :: C++",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Scientific/Engineering :: Medical Science Apps.",
+]
+
+[project.urls]
+"Documentation" = "https://pyncbitk.readthedocs.io/en/stable/"
+"Bug Tracker" = "https://github.com/althonos/pyncbitk/issues"
+"Changelog" = "https://github.com/althonos/pyncbitk/blob/master/CHANGELOG.md"
+"Coverage" = "https://codecov.io/gh/althonos/pyncbitk/"
+"Builds" = "https://github.com/althonos/pyncbitk/actions"
+"PyPI" = "https://pypi.org/project/pyncbitk"
+
+[tool.scikit-build-core-conan]
+path = "."
+build = "missing"
+output-folder = "."
+config = ["tools.cmake.cmaketoolchain:generator=Ninja"]
+settings = ["compiler.cppstd=20"]
+
+[[tool.scikit-build-core-conan.local-recipes]]
+path = "vendor/ncbi-cxx-toolkit-conan"
+name = "ncbi-cxx-toolkit-public"
+version = "29.6.0"
+
+[tool.scikit-build]
+build-dir = "build/{build_type}"
+wheel.py-api = "py3"
+cmake.build-type = "Release"
+
+[[tool.scikit-build-overrides]]
+if.env.SCCACHE = true
+cmake.define.CMAKE_C_COMPILER_LAUNCHER = "sccache"
+cmake.define.CMAKE_CXX_COMPILER_LAUNCHER = "sccache"
+
+[[tool.scikit-build-overrides]]
+if.env.MOLD = true
+cmake.define.CMAKE_LINKER_TYPE = "mold"
+
+[tool.cibuildwheel]
+build-frontend = { name = "build", args = [] }
+build-verbosity = 1
+manylinux-x86_64-image = "althonos/pyncbitk-manylinux_2_34:release"
+
+[tool.cibuildwheel.macos]
+archs = ["x86_64", "arm64"]
+repair-wheel-command = "cp {wheel} {dest_dir}"
+
+[tool.cibuildwheel.macos.environment]
+CC = "/usr/bin/clang"
+CXX = "/usr/bin/clang++"
+MACOSX_DEPLOYMENT_TARGET = "13.3"
+
+[tool.cibuildwheel.linux]
+repair-wheel-command = "auditwheel repair -w {dest_dir} {wheel} --strip --zip-compression-level 9"
+