ncrystal-python 3.9.81__py3-none-any.whl

NCrystal/_hklobjects.py

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+
+################################################################################
+##                                                                            ##
+##  This file is part of NCrystal (see https://mctools.github.io/ncrystal/)   ##
+##                                                                            ##
+##  Copyright 2015-2024 NCrystal developers                                   ##
+##                                                                            ##
+##  Licensed under the Apache License, Version 2.0 (the "License");           ##
+##  you may not use this file except in compliance with the License.          ##
+##  You may obtain a copy of the License at                                   ##
+##                                                                            ##
+##      http://www.apache.org/licenses/LICENSE-2.0                            ##
+##                                                                            ##
+##  Unless required by applicable law or agreed to in writing, software       ##
+##  distributed under the License is distributed on an "AS IS" BASIS,         ##
+##  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.  ##
+##  See the License for the specific language governing permissions and       ##
+##  limitations under the License.                                            ##
+##                                                                            ##
+################################################################################
+
+"""
+
+Experimental feature for more object-oriented and less efficient access to hkl
+lists.
+
+See also https://github.com/mctools/ncrystal/issues/164.
+
+"""
+
+class HKLEntry:
+
+    """A group or family of HKL planes, all sharing the same value of d-spacing
+    and structure factor (fsquared). If .is_symequiv evaluates to True, these
+    exactly represent a group of symmetry-equivalent planes.
+    """
+    def __str__( self ):
+        hkl=self.hkl_label
+        return ( f'HKL( hkl_label=({hkl[0]},{hkl[1]},{hkl[2]}), '
+                 f'd={self.d:g}Aa, F2={self.fsquared:g}barn, '
+                 f'N={self.mult} )' )
+
+    def __init__(self,hh,kk,ll,mult,dsp,fsq,hklinfotype,issymeqv):
+        """For internal usage only, do not create therse objects manually."""
+        self.__h = hh
+        self.__k = kk
+        self.__l = ll
+        self.__mult = mult
+        self.__dsp = dsp
+        self.__fsq = fsq
+        self.__hklinfotype = hklinfotype
+        self.__issymeqv = issymeqv
+
+    @property
+    def hkl_type( self ):
+        """The type of HKL group represented by this entry. Returns
+        HKLInfoType.SymEqvGroup if this is a group of symmetry-equivalent
+        planes.
+        """
+        return self.__hklinfotype
+
+    @property
+    def is_symequiv(self):
+        """Returns True if .hkl_type equals HKLInfoType.SymEqvGroup."""
+        return self.__issymeqv
+
+    @property
+    def hkl_label( self ):
+        """Returns a hkl label for the entry, i.e. one of the hkl points in the
+        group as a tuple of three integers: (h,k,l)."""
+        return (int(self.__h[0]),int(self.__k[0]),int(self.__l[0]))
+
+    @property
+    def h( self ):
+        """
+        An array of h values. Note that this has half the length of
+        .multiplicity, since we exclude entries that can be generated from each
+        other by a mere sign flip.
+        """
+        return self.__h
+
+    @property
+    def k( self ):
+        """
+        An array of k values. Note that this has half the length of
+        .multiplicity, since we exclude entries that can be generated from each
+        other by a mere sign flip.
+        """
+        return self.__k
+
+    @property
+    def l( self ): # noqa E743
+        """
+        An array of l values. Note that this has half the length of
+        .multiplicity, since we exclude entries that can be generated from each
+        other by a mere sign flip.
+        """
+        return self.__l
+
+    @property
+    def dspacing( self ):
+        """The d-spacing value in units of angstrom."""
+        return self.__dsp
+
+    @property
+    def d( self ):
+        """The d-spacing value in units of angstrom."""
+        return self.__dsp
+
+    @property
+    def fsquared( self ):
+        """The squared structure factor (F^2) in units of barn."""
+        return self.__fsq
+
+    @property
+    def f2( self ):
+        """The squared structure factor (F^2) in units of barn."""
+        return self.__fsq
+
+    @property
+    def multiplicity( self ):
+        """The number of hkl points in the group."""
+        return self.__mult
+
+    @property
+    def mult( self ):
+        """The number of hkl points in the group."""
+        return self.__mult
+
+def _iter_hklobjects( info ):
+    hklinfotype = info.hklInfoType()
+    issymeqv = info.hklIsSymEqvGroup()
+    for hh,kk,ll,mult,dsp,fsq in info.hklList(all_indices=True):
+        yield HKLEntry(hh,kk,ll,mult,dsp,fsq,
+                       hklinfotype,issymeqv)
+

NCrystal/_locatelib.py

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+
+################################################################################
+##                                                                            ##
+##  This file is part of NCrystal (see https://mctools.github.io/ncrystal/)   ##
+##                                                                            ##
+##  Copyright 2015-2024 NCrystal developers                                   ##
+##                                                                            ##
+##  Licensed under the Apache License, Version 2.0 (the "License");           ##
+##  you may not use this file except in compliance with the License.          ##
+##  You may obtain a copy of the License at                                   ##
+##                                                                            ##
+##      http://www.apache.org/licenses/LICENSE-2.0                            ##
+##                                                                            ##
+##  Unless required by applicable law or agreed to in writing, software       ##
+##  distributed under the License is distributed on an "AS IS" BASIS,         ##
+##  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.  ##
+##  See the License for the specific language governing permissions and       ##
+##  limitations under the License.                                            ##
+##                                                                            ##
+################################################################################
+
+"""Internal module providing ctypes-based hooks into the compiled NCrystal
+shared library"""
+
+import pathlib
+
+_cache = [None]
+def get_libpath_and_namespace():
+    if _cache[0] is None:
+        _cache[0] = _search()
+    return _cache[0]
+
+def _detect_monolithic_installation():
+    #Determine if these python modules were installed via "pip install
+    #<ncrystalrepo>" (monolithic package with bore core and python parts), or if
+    #using a standard ncrystal-python package. Also detect conflicts in case a
+    #user did both, and thus messed up their environment.
+
+    d = pathlib.Path(__file__).parent
+    is_std = d.joinpath('_is_std.py').is_file()
+    is_mono = d.joinpath('_is_monolithic.py').is_file()
+    assert is_mono or is_std
+    if not ( is_mono and is_std ):
+        return is_mono
+
+    import textwrap
+    conflict_msg = textwrap.dedent("""
+
+    ERROR: Broken environment detected.
+
+    The current environment has traces of both a normal NCrystal installation
+    (where ncrystal-core and ncrystal-python modules are installed separately),
+    and a monolithic installation (most likely from running "pip install"
+    directly on the root of the ncrystal source tree). This latter method is
+    primarily intended for developers, and should never be performed in an
+    environment where NCrystal is already installed through other conventional
+    methods.
+
+    Most likely your environment is now broken. You can attempt to fix it by
+    uninstalling all NCrystal packages (with the same package manager that did
+    the original installation of that package), and then installing NCrystal
+    again from one source only. Or you might simply wish to remove and recreate
+    the environment from scratch.
+    """)
+    #We can not simply emit ImportError, since it might be taken by clients as
+    #"ncrystal not installed". We can choose RuntimeError or SystemExit. To be
+    #100% this triggers a warning, we pick SystemExit.
+    raise SystemExit(conflict_msg)
+
+def _search():
+    #Try to determine the location of the NCrystal shared library. In order of
+    #preference, we try:
+    #
+    #  1) The NCrystal_LIB environment variable (intended for specialised usage,
+    #     like CTests). Normally this variable is also enough for us to be able
+    #     to decode the NCrystal namespace protection used, if any. But if it
+    #     fails, one can use the NCRYSTAL_LIB_NAMESPACE_PROTECTION variable to
+    #     specify it explicitly.
+    #
+    #  2) Attempt to get the location via a python module providing it (in case
+    #     ncrystal-core was installed via PyPI for instance).
+    #
+    #  3) Invoke "ncrystal-config --show ..." for the information.
+    #
+    #  If simplebuild devel mode we allow env var overrides, but apart from that
+    #  always go straight to the ncrystal-config method.
+
+    # Always invoke _detect_monolithic_installation() since it also detects
+    # broken installations.
+    import os
+    verbose = 'NCRYSTAL_DEBUG_LIBSEARCH' in os.environ
+    if verbose:
+        from ._common import print
+        print('NCrystal._locatelib: Starting search for'
+              ' NCrystal shared library')
+    is_monolithic = _detect_monolithic_installation()
+    if verbose:
+        print('NCrystal._locatelib: monolithic installation'
+              f' = {"yes" if is_monolithic else "no"}')
+
+    v = _search_env_overrides()
+    if verbose and v:
+        print('NCrystal._locatelib: Succesfully searched via method: env vars')
+
+    is_simplebuild_devel = ( pathlib.Path(__file__).parent
+                             .joinpath('_is_sblddevel.py').is_file() )
+
+    if not v and not is_simplebuild_devel:
+        v = _search_core_info_mod( is_monolithic )
+        if verbose and v:
+            print('NCrystal._locatelib: Succesfully searched via method: pymod')
+
+    if not v:
+        v = _search_nccfgapp( 'sb_nccmd_config'
+                              if is_simplebuild_devel
+                              else 'ncrystal-config' )
+        if verbose and v:
+            print('NCrystal._locatelib: Succesfully searched'
+                  ' via method: ncrystal-config')
+
+    if not v:
+        from .exceptions import NCFileNotFound
+        raise NCFileNotFound('Could not locate the NCrystal shared library'
+                             ' file. Have you installed the ncrystal-core'
+                             ' package?')
+    lib, namespace, version = v
+    if verbose:
+        print(f'NCrystal._locatelib: namespace = "{namespace}"')
+        print(f'NCrystal._locatelib: lib = "{lib}"')
+
+    lib = pathlib.Path(lib)
+    if not lib.is_file():
+        from .exceptions import NCFileNotFound
+        raise NCFileNotFound('Problems locating the NCrystal shared library'
+                             f' file. Tried "{lib}" unsuccesfully.')
+    version_ok = True
+    if version is not None:
+        from . import __version__ as _nc_version
+        version_ok = _nc_version.strip() == version.strip()
+    if version_ok:
+        return ( lib.absolute().resolve(), ( namespace or '' ) )
+
+    #Found it, but there was a version mismatch!
+    import textwrap
+    msg = textwrap.dedent(f"""
+    ERROR: Inconsistent environment detected.
+
+    The version of the installed core ncrystal modules ({version}) and the
+    ncrystal Python API ({_nc_version}) are not identical. This is not
+    supported.
+    """)
+    #The environment is not necessarily completely broken, but the NCrystal
+    #packages can not be used. Hence, we emit an ImportError here. However, we
+    #also emit a warning, in case the client code is hiding ImportError's, on
+    #the assumption it simply means NCrystal is not available.
+    from ._common import warn
+    warn(msg)
+    raise ImportError(msg)
+
+def _search_env_overrides():
+    import os
+    #NB: The next two variables can NOT be namespaced. E.g. it will always be
+    #NCRYSTAL_LIB, and never e.g. NCRYSTAL<NAMESPACEHERE>_LIB:
+    lib = os.environ.get('NCRYSTAL_LIB')
+
+    #This second variable is hopefully not needed, since the namespace can
+    #hopefully be inferred from the shared library name, but we allow it as an
+    #ultimate fall-back option in case one is for some reason running with
+    #non-standard naming of the shared libraries:
+    ns = os.environ.get('NCRYSTAL_LIB_NAMESPACE_PROTECTION','')
+    if lib:
+        if not ns and '.' in lib and 'NCrystal-' in lib:
+            #Try to infer the namespace from the library name (so it is enough
+            #to set NCRYSTAL_LIB).
+            ll = lib.split('.')[0]
+            if 'NCrystal-' in ll:
+                ll = ll.split('NCrystal-')[-1]
+                if ll and 'NCrystal-' not in ll and '.' not in ll:
+                    ns = ll
+        lib = pathlib.Path(lib)
+        if not lib.exists() or lib.is_dir():
+            from .exceptions import NCFileNotFound
+            raise NCFileNotFound('NCRYSTAL_LIB environment variable is set'
+                                 f' ("{lib}") but does not point'
+                                 ' to an actual file.')
+        return lib, ns, None
+
+def _search_core_info_mod( is_monolithic ):
+    #Look for the standard module, installed by the ncrystal-core package.
+    try:
+        if is_monolithic:
+            import _ncrystal_core_monolithic.info as mod
+        else:
+            import _ncrystal_core.info as mod
+    except ModuleNotFoundError:
+        mod = None
+    if mod:
+        return mod.libpath(), mod.namespace(), mod.version()
+
+def _search_nccfgapp( cmdname ):
+    #Try to query ncrystal-config script:
+    import subprocess
+    res = subprocess.run([cmdname,'--show','shlibpath','namespace','version'],
+                         capture_output=True)
+    if res.returncode == 0:
+        lines = res.stdout.decode('utf8').splitlines()
+        if len(lines) == 3:
+            p = pathlib.Path(lines[0])
+            if p.is_file():
+                return p, ( lines[1].strip() or None ), lines[2].strip()