import os, sys, subprocess, glob import os.path as osp import pathlib import shutil import configparser import sysconfig from setuptools import setup, Extension from setuptools.dist import Distribution from typing import List USE_PY_LIMITED_API = ( # require opt-in (builds are specialized by default) os.getenv('NETCDF4_LIMITED_API', '0') == '1' # Cython + numpy + limited API de facto requires Python >=3.11 and sys.version_info >= (3, 11) # as of Python 3.14t, free-threaded builds don't support the limited API and not sysconfig.get_config_var("Py_GIL_DISABLED") ) ABI3_TARGET_VERSION = "".join(str(_) for _ in sys.version_info[:2]) ABI3_TARGET_HEX = hex(sys.hexversion & 0xFFFF00F0) if USE_PY_LIMITED_API: SETUP_OPTIONS = {"bdist_wheel": {"py_limited_api": f"cp{ABI3_TARGET_VERSION}"}} else: SETUP_OPTIONS = {} open_kwargs = {'encoding': 'utf-8'} def check_hdf5version(hdf5_includedir): try: f = open(os.path.join(hdf5_includedir, 'H5public.h'), **open_kwargs) except OSError: return None hdf5_version = None for line in f: if line.startswith('#define H5_VERS_INFO'): hdf5_version = line.split('"')[1] return hdf5_version def get_hdf5_version(direc): # check to see if hdf5 headers in direc, return version number or None hdf5_version = None print(f"checking {direc}...") hdf5_version = check_hdf5version(direc) if hdf5_version is None: print(f'hdf5 headers not found in {direc}') return None else: print(f'{hdf5_version} headers found in {direc}') return hdf5_version def check_ifnetcdf4(netcdf4_includedir): try: f = open(os.path.join(netcdf4_includedir, 'netcdf.h'), **open_kwargs) except OSError: return False isnetcdf4 = False for line in f: if line.startswith('nc_inq_compound'): isnetcdf4 = True return isnetcdf4 def check_has_parallel_support(inc_dirs: list) -> bool: has_parallel_support = False for d in inc_dirs: ncmetapath = os.path.join(d,'netcdf_meta.h') if not os.path.exists(ncmetapath): continue with open(ncmetapath) as f: for line in f: if line.startswith('#define NC_HAS_PARALLEL'): try: has_parallel_support = bool(int(line.split()[2])) except ValueError: pass return has_parallel_support def getnetcdfvers(libdirs): """ Get the version string for the first netcdf lib found in libdirs. (major.minor.release). If nothing found, return None. """ import os, re, sys, ctypes if sys.platform.startswith('win'): regexp = re.compile('^netcdf.dll$') elif sys.platform.startswith('cygwin'): bindirs = [] for d in libdirs: bindirs.append(os.path.dirname(d) + '/bin') regexp = re.compile(r'^cygnetcdf-\d.dll') elif sys.platform.startswith('darwin'): regexp = re.compile(r'^libnetcdf.dylib') else: regexp = re.compile(r'^libnetcdf.so') if sys.platform.startswith('cygwin'): dirs = bindirs else: dirs = libdirs for d in dirs: try: candidates = [x for x in os.listdir(d) if regexp.match(x)] if len(candidates) != 0: candidates.sort( key=lambda x: len(x)) # Prefer libfoo.so to libfoo.so.X.Y.Z path = os.path.abspath(os.path.join(d, candidates[0])) lib = ctypes.cdll.LoadLibrary(path) inq_libvers = lib.nc_inq_libvers inq_libvers.restype = ctypes.c_char_p vers = lib.nc_inq_libvers() return vers.split()[0] except Exception: pass # We skip invalid entries, because that's what the C compiler does return None def extract_version(CYTHON_FNAME): version = None with open(CYTHON_FNAME) as fi: for line in fi: if (line.startswith('__version__')): _, version = line.split('=') version = version.strip()[1:-1] # Remove quotation characters. break return version HDF5_dir = os.environ.get('HDF5_DIR') HDF5_incdir = os.environ.get('HDF5_INCDIR') HDF5_libdir = os.environ.get('HDF5_LIBDIR') netCDF4_dir = os.environ.get('NETCDF4_DIR') netCDF4_incdir = os.environ.get('NETCDF4_INCDIR') netCDF4_libdir = os.environ.get('NETCDF4_LIBDIR') szip_dir = os.environ.get('SZIP_DIR') szip_libdir = os.environ.get('SZIP_LIBDIR') szip_incdir = os.environ.get('SZIP_INCDIR') hdf4_dir = os.environ.get('HDF4_DIR') hdf4_libdir = os.environ.get('HDF4_LIBDIR') hdf4_incdir = os.environ.get('HDF4_INCDIR') jpeg_dir = os.environ.get('JPEG_DIR') jpeg_libdir = os.environ.get('JPEG_LIBDIR') jpeg_incdir = os.environ.get('JPEG_INCDIR') curl_dir = os.environ.get('CURL_DIR') curl_libdir = os.environ.get('CURL_LIBDIR') curl_incdir = os.environ.get('CURL_INCDIR') mpi_incdir = os.environ.get('MPI_INCDIR') USE_NCCONFIG = bool(int(os.environ.get('USE_NCCONFIG', 0))) # override use of setup.cfg with env var. USE_SETUPCFG = bool(int(os.environ.get('USE_SETUPCFG', 1))) setup_cfg = 'setup.cfg' # contents of setup.cfg will override env vars, unless # USE_SETUPCFG evaluates to False. ncconfig = None use_ncconfig = None if USE_SETUPCFG and os.path.exists(setup_cfg): print('reading from setup.cfg...') config = configparser.ConfigParser() config.read(setup_cfg) HDF5_dir = config.get("directories", "HDF5_dir", fallback=HDF5_dir) HDF5_libdir = config.get("directories", "HDF5_libdir", fallback=HDF5_libdir) HDF5_incdir = config.get("directories", "HDF5_incdir", fallback=HDF5_incdir) netCDF4_dir = config.get("directories", "netCDF4_dir", fallback=netCDF4_dir) netCDF4_libdir = config.get("directories", "netCDF4_libdir", fallback=netCDF4_libdir) netCDF4_incdir = config.get("directories", "netCDF4_incdir", fallback=netCDF4_incdir) szip_dir = config.get("directories", "szip_dir", fallback=szip_dir) szip_libdir = config.get("directories", "szip_libdir", fallback=szip_libdir) szip_incdir = config.get("directories", "szip_incdir", fallback=szip_incdir) hdf4_dir = config.get("directories", "hdf4_dir", fallback=hdf4_dir) hdf4_libdir = config.get("directories", "hdf4_libdir", fallback=hdf4_libdir) hdf4_incdir = config.get("directories", "hdf4_incdir", fallback=hdf4_incdir) jpeg_dir = config.get("directories", "jpeg_dir", fallback=jpeg_dir) jpeg_libdir = config.get("directories", "jpeg_libdir", fallback=jpeg_libdir) jpeg_incdir = config.get("directories", "jpeg_incdir", fallback=jpeg_incdir) curl_dir = config.get("directories", "curl_dir", fallback=curl_dir) curl_libdir = config.get("directories", "curl_libdir", fallback=curl_libdir) curl_incdir = config.get("directories", "curl_incdir", fallback=curl_incdir) mpi_incdir = config.get("directories","mpi_incdir", fallback=mpi_incdir) use_ncconfig = config.getboolean("options", "use_ncconfig", fallback=use_ncconfig) ncconfig = config.get("options", "ncconfig", fallback=ncconfig) try: if ncconfig is None: if netCDF4_dir is not None: ncconfig = os.path.join(netCDF4_dir, 'bin/nc-config') else: # otherwise, just hope it's in the users PATH. ncconfig = 'nc-config' HAS_NCCONFIG = subprocess.call([ncconfig, '--libs']) == 0 except OSError: HAS_NCCONFIG = False # make sure USE_NCCONFIG from environment takes # precedence over use_ncconfig from setup.cfg (issue #341). if use_ncconfig and not USE_NCCONFIG: USE_NCCONFIG = use_ncconfig elif not USE_NCCONFIG: # if nc-config exists, and USE_NCCONFIG not set, try to use it. USE_NCCONFIG = HAS_NCCONFIG try: HAS_PKG_CONFIG = subprocess.call(['pkg-config', '--libs', 'hdf5']) == 0 except OSError: HAS_PKG_CONFIG = False def config_flags(command: List[str], flag: str) -> list: """Pull out specific flags from a config command (pkg-config or nc-config)""" flags = subprocess.run(command, capture_output=True, text=True) return [arg[2:] for arg in flags.stdout.split() if arg.startswith(flag)] def _populate_hdf5_info(dirstosearch, inc_dirs, libs, lib_dirs): global HDF5_incdir, HDF5_dir, HDF5_libdir nohdf5dirs = HDF5_incdir is None and HDF5_libdir is None and HDF5_dir is None if HAS_PKG_CONFIG and nohdf5dirs: # if HDF5 dirs not specified, and pkg-config available, use it inc_dirs.extend(config_flags(["pkg-config", "--cflags", "hdf5"], "-I")) libs.extend(config_flags(["pkg-config", "--libs", "hdf5"], "-l")) lib_dirs.extend(config_flags(["pkg-config", "--libs", "hdf5"], "-L")) else: if HDF5_incdir is None and HDF5_dir is None: print(" HDF5_DIR environment variable not set, checking some standard locations ..") for direc in dirstosearch: hdf5_version = get_hdf5_version(os.path.join(direc, 'include')) if hdf5_version is None: continue else: HDF5_dir = direc HDF5_incdir = os.path.join(direc, 'include') print(f'{hdf5_version} found in {HDF5_dir}') break if HDF5_dir is None: raise ValueError('did not find HDF5 headers') else: if HDF5_incdir is None: HDF5_incdir = os.path.join(HDF5_dir, 'include') hdf5_version = get_hdf5_version(HDF5_incdir) if hdf5_version is None: raise ValueError(f'did not find HDF5 headers in {HDF5_incdir}') print(f'{hdf5_version} found in {HDF5_dir}') if HDF5_libdir is None and HDF5_dir is not None: HDF5_libdir = os.path.join(HDF5_dir, 'lib') if HDF5_libdir is not None: lib_dirs.append(HDF5_libdir) if HDF5_incdir is not None: inc_dirs.append(HDF5_incdir) libs.extend(['hdf5_hl', 'hdf5']) dirstosearch = [] if os.environ.get("CONDA_PREFIX"): dirstosearch.append(os.environ["CONDA_PREFIX"]) # linux,macosx dirstosearch.append(os.path.join(os.environ["CONDA_PREFIX"],'Library')) # windows dirstosearch += [os.path.expanduser('~'), '/usr/local', '/sw', '/opt', '/opt/local', '/opt/homebrew', '/usr'] # try nc-config first if USE_NCCONFIG and HAS_NCCONFIG and ncconfig is not None: print(f'using {ncconfig}...') libs = config_flags([ncconfig, "--libs"], "-l") lib_dirs = config_flags([ncconfig, "--libs"], "-L") inc_dirs = config_flags([ncconfig, '--cflags'], "-I") # check to see if hdf5 found in directories returned by nc-config hdf5_version = None for direc in inc_dirs: hdf5_version = get_hdf5_version(direc) if hdf5_version is not None: if sys.platform == "cygwin": _populate_hdf5_info(dirstosearch, inc_dirs, libs, lib_dirs) break # if hdf5 not found, search other standard locations (including those specified in env vars). if hdf5_version is None: print('nc-config did provide path to HDF5 headers, search standard locations...') _populate_hdf5_info(dirstosearch, inc_dirs, libs, lib_dirs) # If nc-config doesn't work, fall back on brute force method. else: lib_dirs = [] inc_dirs = [] libs = [] # _populate_hdf5_info will use HDF5_dir, HDF5_libdir and HDF5_incdir if they are set. # otherwise pkg-config will be tried, and if that fails, dirstosearch will be searched. _populate_hdf5_info(dirstosearch, inc_dirs, libs, lib_dirs) if netCDF4_incdir is None and netCDF4_dir is None: print("NETCDF4_DIR environment variable not set, checking standard locations..") for direc in dirstosearch: print(f'checking {direc}...') isnetcdf4 = check_ifnetcdf4(os.path.join(direc, 'include')) if not isnetcdf4: continue else: netCDF4_dir = direc netCDF4_incdir = os.path.join(direc, 'include') print(f'netCDF4 found in {netCDF4_dir}') break if netCDF4_dir is None: raise ValueError('did not find netCDF version 4 headers') else: if netCDF4_incdir is None: netCDF4_incdir = os.path.join(netCDF4_dir, 'include') isnetcdf4 = check_ifnetcdf4(netCDF4_incdir) if not isnetcdf4: raise ValueError( 'did not find netCDF version 4 headers %s' % netCDF4_incdir) if netCDF4_libdir is None and netCDF4_dir is not None: netCDF4_libdir = os.path.join(netCDF4_dir, 'lib') if sys.platform == 'win32': libs.extend(['netcdf', 'zlib']) else: libs.extend(['netcdf', 'z']) if netCDF4_libdir is not None: lib_dirs.append(netCDF4_libdir) if netCDF4_incdir is not None: inc_dirs.append(netCDF4_incdir) # add szip to link if desired. if szip_libdir is None and szip_dir is not None: szip_libdir = os.path.join(szip_dir, 'lib') if szip_incdir is None and szip_dir is not None: szip_incdir = os.path.join(szip_dir, 'include') if szip_incdir is not None and szip_libdir is not None: if sys.platform == 'win32': libs.append('szip') else: libs.append('sz') lib_dirs.append(szip_libdir) inc_dirs.append(szip_incdir) # add hdf4 to link if desired. if hdf4_libdir is None and hdf4_dir is not None: hdf4_libdir = os.path.join(hdf4_dir, 'lib') if hdf4_incdir is None and hdf4_dir is not None: hdf4_incdir = os.path.join(hdf4_dir, 'include') if hdf4_incdir is not None and hdf4_libdir is not None: libs.append('mfhdf') libs.append('df') lib_dirs.append(hdf4_libdir) inc_dirs.append(hdf4_incdir) # add jpeg to link if desired. if jpeg_libdir is None and jpeg_dir is not None: jpeg_libdir = os.path.join(jpeg_dir, 'lib') if jpeg_incdir is None and jpeg_dir is not None: jpeg_incdir = os.path.join(jpeg_dir, 'include') if jpeg_incdir is not None and jpeg_libdir is not None: libs.append('jpeg') lib_dirs.append(jpeg_libdir) inc_dirs.append(jpeg_incdir) # add curl to link if desired. if curl_libdir is None and curl_dir is not None: curl_libdir = os.path.join(curl_dir, 'lib') if curl_incdir is None and curl_dir is not None: curl_incdir = os.path.join(curl_dir, 'include') if curl_incdir is not None and curl_libdir is not None: libs.append('curl') lib_dirs.append(curl_libdir) inc_dirs.append(curl_incdir) # Do not require numpy for just querying the package # Taken from the h5py setup file. if any('--' + opt in sys.argv for opt in Distribution.display_option_names + ['help-commands', 'help']) or sys.argv[1] == 'egg_info': pass else: # append numpy include dir. import numpy inc_dirs.append(numpy.get_include()) # get netcdf library version. netcdf_lib_version = getnetcdfvers(lib_dirs) if netcdf_lib_version is None: print('unable to detect netcdf library version') else: netcdf_lib_version = str(netcdf_lib_version) print(f'using netcdf library version {netcdf_lib_version}') DEFINE_MACROS = [("NPY_NO_DEPRECATED_API", "NPY_1_7_API_VERSION")] netcdf4_src_root = osp.join(osp.join('src','netCDF4'), '_netCDF4') netcdf4_src_c = netcdf4_src_root + '.c' netcdf4_src_pyx = netcdf4_src_root + '.pyx' if 'sdist' not in sys.argv[1:] and 'clean' not in sys.argv[1:] and '--version' not in sys.argv[1:]: print('using Cython to compile netCDF4.pyx...') # remove _netCDF4.c file if it exists, so cython will recompile _netCDF4.pyx. # run for build *and* install (issue #263). Otherwise 'pip install' will # not regenerate _netCDF4.c, even if the C lib supports the new features. if len(sys.argv) >= 2: if os.path.exists(netcdf4_src_c): os.remove(netcdf4_src_c) # for netcdf 4.4.x CDF5 format is always enabled. if netcdf_lib_version is not None and\ (netcdf_lib_version > "4.4" and netcdf_lib_version < "4.5"): has_cdf5_format = True has_parallel_support = check_has_parallel_support(inc_dirs) has_has_not = "has" if has_parallel_support else "does not have" print(f"netcdf lib {has_has_not} parallel functions") if has_parallel_support: try: import mpi4py except ImportError: msg = "Parallel support requires mpi4py but it is not installed." raise ImportError(msg) inc_dirs.append(mpi4py.get_include()) # mpi_incdir should not be needed if using nc-config # (should be included in nc-config --cflags) if mpi_incdir is not None: inc_dirs.append(mpi_incdir) # Name of file containing imports required for parallel support parallel_support_imports = "parallel_support_imports.pxi.in" else: parallel_support_imports = "no_parallel_support_imports.pxi.in" # Copy the specific version of the file containing parallel # support imports shutil.copyfile( osp.join("include", parallel_support_imports), osp.join("include", "parallel_support_imports.pxi") ) nc_complex_dir = pathlib.Path("./external/nc_complex") source_files = [ netcdf4_src_pyx, str(nc_complex_dir / "src/nc_complex.c"), ] include_dirs = inc_dirs + [ "include", str(nc_complex_dir / "include"), str(nc_complex_dir / "include/generated_fallbacks"), ] DEFINE_MACROS += [("NC_COMPLEX_NO_EXPORT", "1")] if USE_PY_LIMITED_API: DEFINE_MACROS.append(("Py_LIMITED_API", ABI3_TARGET_HEX)) ext_modules = [Extension("netCDF4._netCDF4", source_files, define_macros=DEFINE_MACROS, libraries=libs, library_dirs=lib_dirs, include_dirs=include_dirs, py_limited_api=USE_PY_LIMITED_API)] # set language_level directive to 3 for e in ext_modules: e.cython_directives = {'language_level': "3"} # else: ext_modules = None # if NETCDF_PLUGIN_DIR set, install netcdf-c compression plugins inside package # (should point to location of lib__nc* files built by netcdf-c) copied_plugins=False if os.environ.get("NETCDF_PLUGIN_DIR"): plugin_dir = os.environ.get("NETCDF_PLUGIN_DIR") plugins = glob.glob(os.path.join(plugin_dir, "lib__nc*")) if not plugins: print('no plugin files in NETCDF_PLUGIN_DIR, not installing...') data_files = [] else: data_files = plugins print(f'installing netcdf compression plugins from {plugin_dir} ...') sofiles = [os.path.basename(sofilepath) for sofilepath in data_files] print(repr(sofiles)) if 'sdist' not in sys.argv[1:] and 'clean' not in sys.argv[1:] and '--version' not in sys.argv[1:]: for f in data_files: shutil.copy(f, osp.join(os.getcwd(),osp.join(osp.join('src','netCDF4'),'plugins'))) copied_plugins=True else: print('NETCDF_PLUGIN_DIR not set, no netcdf compression plugins installed') data_files = [] # See pyproject.toml for project metadata setup( name="netCDF4", # need by GitHub dependency graph version=extract_version(netcdf4_src_pyx), ext_modules=ext_modules, options=SETUP_OPTIONS, ) # remove plugin files copied from outside source tree if copied_plugins: for f in sofiles: filepath = osp.join(osp.join(osp.join('src','netCDF4'),'plugins'),f) if os.path.exists(filepath): os.remove(filepath)