NCBI C++ Toolkit v27.0.0

recipes/ncbi-cxx-toolkit-public/all/conandata.yml

@@ -0,0 +1,13 @@
+sources:
+  "27.0.0":
+    url: "https://github.com/ncbi/ncbi-cxx-toolkit-public/archive/refs/tags/release-27.0.0.tar.gz"
+    sha256: "c8fb3f99c6fce4f170b381f3a7789c76a2ff1c23c094c9852e2e3de1fdc57277"
+
+patches:
+  "27.0.0":
+    - patch_file: "patches/27.0.0-compiler.patch"
+      patch_description: "Corrected version check of GCC compiler"
+      patch_type: "portability"
+    - patch_file: "patches/27.0.0-install.patch"
+      patch_description: "Replaced hard-coded configuration with cmake generator expression"
+      patch_type: "conan"

recipes/ncbi-cxx-toolkit-public/all/conanfile.py

@@ -0,0 +1,313 @@
+from conan import ConanFile, conan_version
+from conan.errors import ConanInvalidConfiguration, ConanException
+from conan.tools.microsoft import check_min_vs, is_msvc_static_runtime, is_msvc
+from conan.tools.files import apply_conandata_patches, export_conandata_patches, get, copy, replace_in_file
+from conan.tools.build import check_min_cppstd, cross_building, can_run
+from conan.tools.scm import Version
+from conan.tools.cmake import CMakeDeps, CMakeToolchain, CMake, cmake_layout
+from conan.tools.env import VirtualRunEnv, VirtualBuildEnv
+import os
+import yaml
+import re
+
+required_conan_version = ">=1.53.0"
+
+
+class NcbiCxxToolkit(ConanFile):
+    name = "ncbi-cxx-toolkit-public"
+    description = "NCBI C++ Toolkit -- a cross-platform application framework and a collection of libraries for working with biological data."
+    license = "CC0-1.0"
+    url = "https://github.com/conan-io/conan-center-index"
+    homepage = "https://ncbi.github.io/cxx-toolkit"
+    topics = ("ncbi", "biotechnology", "bioinformatics", "genbank", "gene",
+              "genome", "genetic", "sequence", "alignment", "blast",
+              "biological", "toolkit", "c++")
+    package_type = "library"
+    settings = "os", "arch", "compiler", "build_type"
+    options = {
+        "shared":     [True, False],
+        "fPIC":       [True, False],
+        "with_targets":  ["ANY"],
+        "with_components": ["ANY"]
+    }
+    default_options = {
+        "shared":     False,
+        "fPIC":       True,
+        "with_targets":   "",
+        "with_components": ""
+    }
+    short_paths = True
+    _dependencies = None
+    _requirements = None
+    _componenttargets = set()
+
+    @property
+    def _min_cppstd(self):
+        return 17
+
+    @property
+    def _compilers_minimum_version(self):
+        return {
+            "gcc": "7",
+            "clang": "7",
+            "apple-clang": "10",
+        }
+
+    @property
+    def _dependencies_folder(self):
+        return "dependencies"
+
+    @property
+    def _dependencies_filename(self):
+        return f"dependencies-{Version(self.version).major}.{Version(self.version).minor}.yml"
+
+    @property
+    def _requirements_filename(self):
+        return f"requirements-{Version(self.version).major}.{Version(self.version).minor}.yml"
+
+    @property
+    def _tk_dependencies(self):
+        if self._dependencies is None:
+            dependencies_filepath = os.path.join(self.recipe_folder, self._dependencies_folder, self._dependencies_filename)
+            if not os.path.isfile(dependencies_filepath):
+                raise ConanException(f"Cannot find {dependencies_filepath}")
+            with open(dependencies_filepath, "r", encoding="utf-8") as f:
+                self._dependencies = yaml.safe_load(f)
+        return self._dependencies
+
+    @property
+    def _tk_requirements(self):
+        if self._requirements is None:
+            requirements_filepath = os.path.join(self.recipe_folder, self._dependencies_folder, self._requirements_filename)
+            if not os.path.isfile(requirements_filepath):
+                raise ConanException(f"Cannot find {requirements_filepath}")
+            with open(requirements_filepath, "r", encoding="utf-8") as f:
+                self._requirements = yaml.safe_load(f)
+        return self._requirements
+
+    def _translate_req(self, key):
+        if "Boost" in key:
+            key = "Boost"
+        if key == "BerkeleyDB" and conan_version.major > "1":
+            return None
+        if key in self._tk_requirements["disabled"].keys():
+            if self.settings.os in self._tk_requirements["disabled"][key]:
+                return None
+        if key in self._tk_requirements["requirements"].keys():
+            return self._tk_requirements["requirements"][key]
+        return None
+
+    def _parse_option(self, data):
+        _res = set()
+        if data != "":
+            _data = str(data)
+            _data = _data.replace(",", ";")
+            _data = _data.replace(" ", ";")
+            _res.update(_data.split(";"))
+            if "" in _res:
+                _res.remove("")
+        return _res
+
+    def export(self):
+        copy(self, self._dependencies_filename,
+            os.path.join(self.recipe_folder, self._dependencies_folder),
+            os.path.join(self.export_folder, self._dependencies_folder))
+        copy(self, self._requirements_filename,
+            os.path.join(self.recipe_folder, self._dependencies_folder),
+            os.path.join(self.export_folder, self._dependencies_folder))
+
+    def export_sources(self):
+        export_conandata_patches(self)
+
+    def config_options(self):
+        if self.settings.os == "Windows":
+            del self.options.fPIC
+
+    def configure(self):
+        if self.options.shared:
+            self.options.rm_safe("fPIC")
+
+    def layout(self):
+        cmake_layout(self, src_folder="src")
+
+    def requirements(self):
+        _alltargets = self._parse_option(self.options.with_targets)
+        _required_components = set()
+        for _t in _alltargets:
+            _re = re.compile(_t)
+            for _component in self._tk_dependencies["components"]:
+                _libraries = self._tk_dependencies["libraries"][_component]
+                for _lib in _libraries:
+                    if _re.match(_lib) != None:
+                        _required_components.add(_component)
+                        break
+
+        _allcomponents = self._parse_option(self.options.with_components)
+        _required_components.update(_allcomponents)
+
+        if len(_required_components) > 0:
+            _todo = _required_components.copy()
+            _required_components.clear()
+            _next = set()
+            while len(_todo) > 0:
+                for _component in _todo:
+                    if not _component in _required_components:
+                        _required_components.add(_component)
+                        if _component in self._tk_dependencies["dependencies"].keys():
+                            for _n in self._tk_dependencies["dependencies"][_component]:
+                                if not _n in _required_components:
+                                    _next.add(_n)
+                _todo = _next.copy()
+                _next.clear()
+
+        if len(_required_components) == 0:
+            _required_components.update( self._tk_dependencies["components"])
+        for component in _required_components:
+            self._componenttargets.update(self._tk_dependencies["libraries"][component])
+
+        requirements = set()
+        for component in _required_components:
+            libraries = self._tk_dependencies["libraries"][component]
+            for lib in libraries:
+                if lib in self._tk_dependencies["requirements"].keys():
+                    requirements.update(self._tk_dependencies["requirements"][lib])
+
+        for req in requirements:
+            pkgs = self._translate_req(req)
+            if pkgs != None:
+                for pkg in pkgs:
+                    self.requires(pkg)
+
+    def validate(self):
+        if self.settings.compiler.cppstd:
+            check_min_cppstd(self, self._min_cppstd)
+        if self.settings.os not in ["Linux", "Macos", "Windows"]:
+            raise ConanInvalidConfiguration("This operating system is not supported")
+        if is_msvc(self):
+            check_min_vs(self, 192)
+            if self.options.shared and is_msvc_static_runtime(self) and Version(self.version) < "28":
+                raise ConanInvalidConfiguration("This configuration is not supported")
+        else:
+            minimum_version = self._compilers_minimum_version.get(str(self.settings.compiler), False)
+            if minimum_version and Version(self.settings.compiler.version) < minimum_version:
+                raise ConanInvalidConfiguration(f"This version of {self.settings.compiler} is not supported")
+        if cross_building(self):
+            raise ConanInvalidConfiguration("Cross compilation is not supported")
+
+    def source(self):
+        get(self, **self.conan_data["sources"][self.version], strip_root=True)
+
+    def generate(self):
+        tc = CMakeToolchain(self)
+        tc.variables["NCBI_PTBCFG_PACKAGING"] = True
+        if self.options.shared:
+            tc.variables["NCBI_PTBCFG_ALLOW_COMPOSITE"] = True
+        tc.variables["NCBI_PTBCFG_PROJECT_LIST"] = "-app/netcache"
+        if self.options.with_targets != "":
+            tc.variables["NCBI_PTBCFG_PROJECT_TARGETS"] = self.options.with_targets
+        if len(self._componenttargets) != 0:
+            tc.variables["NCBI_PTBCFG_PROJECT_COMPONENTTARGETS"] = ";".join(self._componenttargets)
+        if is_msvc(self):
+            tc.variables["NCBI_PTBCFG_CONFIGURATION_TYPES"] = self.settings.build_type
+        tc.variables["NCBI_PTBCFG_PROJECT_TAGS"] = "-demo;-sample"
+        tc.generate()
+        CMakeDeps(self).generate()
+        VirtualBuildEnv(self).generate()
+        if can_run(self):
+            VirtualRunEnv(self).generate(scope="build")
+
+    def _patch_sources(self):
+        apply_conandata_patches(self)
+        if self.settings.os == "Macos":
+            grpc = os.path.join(self.source_folder, "src", "build-system", "cmake", "CMake.NCBIptb.grpc.cmake")
+            replace_in_file(self, grpc,
+                "COMMAND ${_cmd}",
+                "COMMAND ${CMAKE_COMMAND} -E env \"DYLD_LIBRARY_PATH=$ENV{DYLD_LIBRARY_PATH}\" ${_cmd}")
+        root = os.path.join(self.source_folder, "CMakeLists.txt")
+        with open(root, "w", encoding="utf-8") as f:
+            f.write("cmake_minimum_required(VERSION 3.15)\n")
+            f.write("project(ncbi-cpp)\n")
+            f.write("include(src/build-system/cmake/CMake.NCBItoolkit.cmake)\n")
+            f.write("add_subdirectory(src)\n")
+
+    def build(self):
+        self._patch_sources()
+        cmake = CMake(self)
+        cmake.configure()
+# Visual Studio sometimes runs "out of heap space"
+#        if is_msvc(self):
+#            cmake.parallel = False
+        cmake.build()
+
+    def package(self):
+        cmake = CMake(self)
+        cmake.install()
+
+    @property
+    def _module_file_rel_path(self):
+        return os.path.join("res", "build-system", "cmake", "CMake.NCBIpkg.conan.cmake")
+
+    def package_info(self):
+        impfile = os.path.join(self.package_folder, "res", "ncbi-cpp-toolkit.imports")
+        with open(impfile, "r", encoding="utf-8") as f:
+            allexports = set(f.read().split()).intersection(self._componenttargets)
+        absent = []
+        for component in self._tk_dependencies["components"]:
+            c_libs = []
+            libraries = self._tk_dependencies["libraries"][component]
+            for lib in libraries:
+                if lib in allexports:
+                    c_libs.append(lib)
+            if len(c_libs) == 0 and len(libraries) != 0:
+                absent.append(component)
+        for component in self._tk_dependencies["components"]:
+            c_libs = []
+            c_reqs = []
+            n_reqs = set()
+            c_deps = self._tk_dependencies["dependencies"][component]
+            for c in c_deps:
+                if c in absent:
+                    c_deps.remove(c)
+            c_reqs.extend(c_deps)
+            libraries = self._tk_dependencies["libraries"][component]
+            for lib in libraries:
+                if lib in allexports:
+                    c_libs.append(lib)
+                if lib in self._tk_dependencies["requirements"].keys():
+                    n_reqs.update(self._tk_dependencies["requirements"][lib])
+            for req in n_reqs:
+                pkgs = self._translate_req(req)
+                if pkgs != None:
+                    for pkg in pkgs:
+                        pkg = pkg[:pkg.find("/")]
+                        ref = pkg + "::" + pkg
+                        c_reqs.append(ref)
+            if len(c_libs) != 0 or (len(libraries) == 0 and len(c_reqs) != 0):
+                self.cpp_info.components[component].libs = c_libs
+                self.cpp_info.components[component].requires = c_reqs
+
+        if self.settings.os == "Windows":
+            self.cpp_info.components["core"].defines.append("_UNICODE")
+            self.cpp_info.components["core"].defines.append("_CRT_SECURE_NO_WARNINGS=1")
+        else:
+            self.cpp_info.components["core"].defines.append("_MT")
+            self.cpp_info.components["core"].defines.append("_REENTRANT")
+            self.cpp_info.components["core"].defines.append("_THREAD_SAFE")
+            self.cpp_info.components["core"].defines.append("_FILE_OFFSET_BITS=64")
+        if self.options.shared:
+            self.cpp_info.components["core"].defines.append("NCBI_DLL_BUILD")
+        if self.settings.build_type == "Debug":
+            self.cpp_info.components["core"].defines.append("_DEBUG")
+        else:
+            self.cpp_info.components["core"].defines.append("NDEBUG")
+        if self.settings.os == "Windows":
+            self.cpp_info.components["core"].system_libs = ["ws2_32", "dbghelp"]
+        elif self.settings.os == "Linux":
+            self.cpp_info.components["core"].system_libs = ["dl", "rt", "m", "pthread", "resolv"]
+        elif self.settings.os == "Macos":
+            self.cpp_info.components["core"].system_libs = ["dl", "c", "m", "pthread", "resolv"]
+            self.cpp_info.components["core"].frameworks = ["ApplicationServices"]
+        self.cpp_info.components["core"].builddirs.append("res")
+        build_modules = [self._module_file_rel_path]
+        self.cpp_info.components["core"].build_modules = build_modules
+        self.cpp_info.set_property("cmake_build_modules", build_modules)