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conanfile.py
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conanfile.py
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import os
from conans import CMake, ConanFile, tools
from conans.errors import ConanException
class Pod5Conan(ConanFile):
name = "pod5_file_format"
license = "MPL 2.0"
url = "https://github.com/nanoporetech/pod5-file-format"
description = "POD5 File format"
topics = "arrow"
settings = "os", "compiler", "build_type", "arch"
options = {"shared": [True, False], "nanopore_internal_build": [True, False]}
_cmake = None
default_options = {
"shared": False,
"nanopore_internal_build": False,
"boost:header_only": True,
}
generators = "cmake_find_package_multi"
exports_sources = [
"c++/*",
"cmake/*",
"python/*",
"third_party/*",
"CMakeLists.txt",
"LICENSE.md",
]
def printSettings(self):
# Print important settings, useful for debugging.
self.output.warn("Pod5Conan: self.settings.os = " + str(self.settings.os))
self.output.warn(
"Pod5Conan: tools.is_apple_os(self.settings.os) = "
+ str(tools.is_apple_os(self.settings.os))
)
self.output.warn("Pod5Conan: self.settings.arch = " + str(self.settings.arch))
try:
self.output.warn(
"Pod5Conan: self.settings.os.sdk = " + str(self.settings.os.sdk)
)
except ConanException:
self.output.warn(
"Pod5Conan: self.settings.os.sdk does not exist (Exception)"
)
self.output.warn(
"Pod5Conan: self.settings.compiler = " + str(self.settings.compiler)
)
try:
self.output.warn(
"Pod5Conan: self.settings.os.version = " + str(self.settings.os.version)
)
except ConanException:
self.output.warn(
"Pod5Conan: self.settings.os.version does not exist (Exception)"
)
try:
self.output.warn(
"Pod5Conan: self.settings.os.sdk = " + str(self.settings.os.sdk)
)
except ConanException:
self.output.warn(
"Pod5Conan: self.settings.os.sdk does not exist (Exception)"
)
def setVersionsAndSuffixes(self):
self.package_suffix = ""
self.arrow_version = "8.0.0"
self.boost_version = "1.78.0"
if self.options.nanopore_internal_build:
self.output.warn(
"Pod5Conan: setVersionsAndSuffixes for internal build, add .1"
)
self.package_suffix = "@nanopore/stable"
self.arrow_version = f"{self.arrow_version}.3"
self.boost_version = f"{self.boost_version}.1"
else:
self.output.warn(
"Pod5Conan: setVersionsAndSuffixes, not for internal build"
)
self.output.warn("Pod5Conan: package_suffix = " + self.package_suffix)
self.output.warn("Pod5Conan: arrow_version = " + self.arrow_version)
self.output.warn("Pod5Conan: boost_version = " + self.boost_version)
def requirements(self):
self.output.warn("Pod5Conan: self.requirements has been called, optional.")
self.setVersionsAndSuffixes()
self.requires(f"arrow/{self.arrow_version}{self.package_suffix}")
self.requires(f"boost/{self.boost_version}{self.package_suffix}")
self.requires(f"flatbuffers/2.0.0{self.package_suffix}")
self.requires(f"zstd/1.5.4{self.package_suffix}")
self.requires(f"zlib/1.2.13{self.package_suffix}")
if not (
self.settings.os == "Windows"
or self.settings.os == "Macos"
or self.settings.os == "iOS"
):
self.requires(f"jemalloc/5.2.1{self.package_suffix}")
self.output.warn("Pod5Conan: self.requirements, requires jemalloc")
else:
self.output.warn("Pod5Conan: self.requirements, does not require jemalloc")
self.output.warn(
f"Pod5Conan: self.requirements, tools.is_apple_os(self.settings.os) = "
f"{tools.is_apple_os(self.settings.os)}"
)
self.output.warn(
f"Pod5Conan: self.requirements, self.settings.os = {self.settings.os}"
)
self.output.warn("Pod5Conan: self.requirements, before printing settings")
self.printSettings()
self.output.warn("Pod5Conan: self.requirements, after printing settings")
def package_id(self):
self.output.warn("Pod5Conan: Calling self.package_id")
# Windows configurations do not specify a C++ standard version.
if self.settings.os == "Windows":
del self.info.settings.compiler.cppstd
result = super().package_id()
self.output.warn(f"Pod5Conan: Called super.package_id, returns {result}")
return result
def compatibility(self):
self.output.warn("Pod5Conan: Calling compatibility")
# Packages that are built with C++14 should be compatible with clients that use C++17 & 20.
if self.settings.compiler.cppstd in ["17", "20"]:
result = [{"settings": [("compiler.cppstd", "14")]}]
else:
result = super().compatibility()
self.output.warn("Pod5Conan: Called compatibility")
return result
def build_requirements(self):
self.output.warn(
"Pod5Conan: self.build_requirements has been called, optional."
)
# When cross compiling we need pre compiled flatbuffers for flatc to run on the build machine
# which is not the target.
#
# The flatbuffers version is most likely available already; it is on the master branch and
# quite likely already built on the development branch. However, it seems that conan
# doesn't realise this since it is the same package that it tries to build, even though it
# is a different revision, flatbuffers on the other hand is downloaded.
self.setVersionsAndSuffixes()
if hasattr(self, "settings_build") and tools.cross_building(self):
self.output.warn(
"Pod5Conan: self.build_requirements, cross-building the build part"
)
self.output.warn(
"Pod5Conan: self.build_requirements, adding requirement for same package"
)
# self.build_requires('pod5_file_format/{}@nanopore/stable'.format(self.version))
self.build_requires(f"flatbuffers/2.0.0{self.package_suffix}")
else:
self.output.warn("Pod5Conan: self.build_requirements, not cross-building")
def generate(self):
self.output.warn("Pod5Conan: self.generate has been called, optional")
def _configure_cmake(self):
if self._cmake:
return self._cmake
self._cmake = CMake(self)
self._cmake.definitions["ENABLE_CONAN"] = "ON"
self._cmake.definitions["BUILD_PYTHON_WHEEL"] = "OFF"
self._cmake.definitions["INSTALL_THIRD_PARTY"] = "OFF"
self._cmake.definitions["POD5_DISABLE_TESTS"] = "ON"
self._cmake.definitions["POD5_BUILD_EXAMPLES"] = "OFF"
self._cmake.definitions["BUILD_SHARED_LIB"] = (
"ON" if self.options.shared else "OFF"
)
self._cmake.configure()
return self._cmake
def configure(self):
self.output.warn("Pod5Conan: Calling self.configure.")
if self.options.nanopore_internal_build:
self.options["boost"].header_only = False
# ensure that linking against pod5 doesn't override the global allocator
self.options["jemalloc"].prefix = "je_"
def build(self):
self.output.warn("Pod5Conan: Calling self.build, required.")
self.output.warn("Pod5Conan: self.build, before printing settings")
self.printSettings()
self.output.warn("Pod5Conan: self.build, after printing settings")
# When cross building, we cannot build the "examples". Change a file in the build directory
# for this version, file CMakeLists.txt at the top level. Note there are several
# CMakeLists.txt in various places, it's the one at the top level. Change line from
#
# option(POD5_BUILD_EXAMPLES "Disable building all examples" ON)
# to
# option(POD5_BUILD_EXAMPLES "Disable building all examples" OFF)
#
# Note that the comment is misleading: ON turns buildin examples on, OFF turns building
# examples off. And note that this must be done before calling _configure_cmake() otherwise
# it will have no effect anymore.
if tools.cross_building(self):
self.output.warn(
"Pod5Conan: Starting to patch CMakeLists.txt, changing POD5_BUILD_EXAMPLES"
)
fileToPatchName = os.path.join(self.source_folder, "CMakeLists.txt")
oldString = 'option(POD5_BUILD_EXAMPLES "Disable building all examples" ON)'
newString = (
'option(POD5_BUILD_EXAMPLES "Disable building all examples" OFF)'
)
with open(fileToPatchName, "r+") as text_file:
file_content = text_file.read()
new_content = file_content.replace(oldString, newString)
text_file.seek(0)
text_file.truncate(0)
text_file.write(new_content)
self.output.warn(
"Pod5Conan: Finished to patch CMakeLists.txt, changing POD5_BUILD_EXAMPLES"
)
self.output.warn(
"Pod5Conan: If there are linker errors complaining about find_all_read_ids,"
)
self.output.warn(
"Pod5Conan: check whether CMakeLists.txt in the build directory has"
)
self.output.warn("Pod5Conan: been changed correctly.")
cmake = self._configure_cmake()
self.output.warn(
"Pod5Conan: cmake.command_line = {}".format(cmake.command_line)
)
self.output.warn(
"Pod5Conan: cmake.build_config = {}".format(cmake.build_config)
)
cmake.build()
def package(self):
self.output.warn("Pod5Conan: Calling self.package, required.")
cmake = self._configure_cmake()
cmake.install()
# Copy the license files
self.copy("LICENSE.md", src=".", dst="licenses")
def package_info(self):
# Note: package_info collects information in self.cpp_info. It is called from the Conan
# application.
#
# This call is made immediately after the pre_package_info hook and before the
# post_package_info hook. To get more information, we can "import traceback" and "import inspect",
# then call traceback.print_stack() to print the complete call stack, or examine
# inspect.stack().
#
# The caller has created self.cpp_info with the name set to the name of self, with a rootpath,
# version and description from self, env_info and user_info set with default values,
# public_deps set to an array with the names of public requirements in conanfile.requires.items.
self.output.warn(
"Calling Pod5Conan package_info from _call_package_info via _handle_node_cache "
"in conans/client/installer.py"
)
self.output.warn(f"Pod5Conan: cpp_info = {self.cpp_info}")
# We would like to inspect self.cpp_info to see the contents, but it is not iterable.
# self.output.warn(
# f"Pod5Conan: cpp_info members = {inspect.getmembers(self.cpp_info)}"
# )
self.output.warn(f"Pod5Conan: cpp_info.rootpath = {self.cpp_info.rootpath}")
self.output.warn(f"Pod5Conan: cpp_info.version = {self.cpp_info.version}")
self.output.warn(
f"Pod5Conan: cpp_info.description = {self.cpp_info.description}"
)
# This creates an error: self.cpp_info.components cannot be used with self.cpp_info
# configs (release/debug/...) at the same time
# self.output.warn(f"Pod5Conan: cpp_info.env_info = {self.cpp_info.env_info}")
# self.output.warn(f"Pod5Conan: cpp_info.user_info = {self.cpp_info.user_info}")
self.output.warn(
f"Pod5Conan: cpp_info.public_deps = {self.cpp_info.public_deps}"
)
# Additions for this package. Note that everything in requirements needs to be mentioned
# here. Except for Windows and Macos, jemalloc is also needed.
self.cpp_info.libs = tools.collect_libs(self)
self.cpp_info.requires = [
"arrow::arrow",
"boost::headers",
"flatbuffers::flatbuffers",
"zstd::zstd",
"zlib::zlib",
]
if not (
self.settings.os == "Windows"
or self.settings.os == "Macos"
or self.settings.os == "iOS"
):
self.cpp_info.requires.append("jemalloc::jemalloc")
super().package_info()
def run(
self,
command,
output=True,
cwd=None,
win_bash=False,
subsystem=None,
msys_mingw=True,
ignore_errors=False,
run_environment=False,
with_login=True,
env="conanbuild",
):
self.output.warn("Calling Pod5Conan run")
self.output.warn("Calling Pod5Conan run, command = " + command)
if output is not True:
self.output.warn("Calling Pod5Conan run, output = " + output)
if cwd is not None:
self.output.warn("Calling Pod5Conan run, cwd = " + cwd)
if win_bash is not False:
self.output.warn("Calling Pod5Conan run, win_bash = " + win_bash)
if subsystem is not None:
self.output.warn("Calling Pod5Conan run, subsystem = " + subsystem)
if msys_mingw is not True:
self.output.warn("Calling Pod5Conan run, msys_mingw = " + msys_mingw)
if ignore_errors is not False:
self.output.warn("Calling Pod5Conan run, ignore_errors = " + ignore_errors)
if run_environment is not False:
self.output.warn(
"Calling Pod5Conan run, run_environment = " + run_environment
)
if with_login is not True:
self.output.warn("Calling Pod5Conan run, with_login = " + with_login)
if env != "conanbuild":
self.output.warn("Calling Pod5Conan run, env = " + env)
super().run(
command=command,
output=output,
cwd=cwd,
win_bash=win_bash,
subsystem=subsystem,
msys_mingw=msys_mingw,
ignore_errors=ignore_errors,
run_environment=run_environment,
with_login=with_login,
env=env,
)
def test(self):
self.output.warn("Pod5Conan: Calling self.test")
if tools.cross_building(self):
self.output.warn(
"Pod5Conan: self.test not performed because cross_building"
)
return
self.output.warn("Pod5Conan: self.test performed because not cross_building")
return super().test()