__all__ = ["use_old_api", "use_new_api", "use_mixed_api"]
def _upper_split(data):
"""
Thanks to this stackoverflow post for the inspiration
https://stackoverflow.com/questions/7322028/how-to-replace-uppercase-with-underscore
"""
buff = ""
for item in data:
if item.isupper():
if buff:
if buff == "An" or buff == "A":
buff = ""
else:
yield buff
buff = ""
buff += item
yield buff
def _pythonize(C, delete_old: bool = True) -> None:
"""Pythonize the passed class. This will rename the functions
so that they better match the Python style
(changing mixedCase function names into underscore_case)
This makes the change with full awareness of the naming
convention used in sire. This includes changing
cutGroup to cutgroup and typeName to typename,
and nSomething to num_something. This ignores functions
that start with an underscore.
Note that this changes the API of the class globally.
All objects created from this class (and to be created)
will now have the new API. The old API is deleted.
Args:
C
The Class type to be pythonized
delete_old: bool (defaults to True)
Whether or not to remove the old function name.
Returns:
None
"""
if type(C) is list:
for CLS in C:
_pythonize(CLS)
return
import re
for attr in dir(C):
if attr.startswith("_"):
continue
new_attr = attr
# change typeName into typename
if attr == "typeName":
new_attr = "typename"
# change 'cutGroup' into 'cutgroup'
new_attr = new_attr.replace("utGroup", "utgroup")
# change 'LJ' into 'lj'
if new_attr.find("LJ") != -1:
if new_attr == "LJ":
new_attr = "lj"
elif new_attr.startswith("LJ"):
new_attr = new_attr.replace("LJ", "lj_")
elif new_attr.endswith("LJ"):
new_attr = new_attr.replace("LJ", "_lj")
else:
new_attr = new_attr.replace("LJ", "_lj_")
if new_attr.startswith("asAn"):
new_attr = new_attr.replace("asAn", "as")
elif new_attr.startswith("asA"):
new_attr = new_attr.replace("asA", "as")
elif new_attr.startswith("isAn"):
new_attr = new_attr.replace("isAn", "is")
elif new_attr.startswith("isAtom"):
new_attr = new_attr.replace("isAtom", "is_atom")
elif new_attr.startswith("isA"):
new_attr = new_attr.replace("isA", "is")
# change 'ID()' into 'id()'
if new_attr == "ID":
new_attr = "id"
elif new_attr == "IDs":
new_attr = "ids"
# change all caps into lowercase
if new_attr.isupper():
new_attr = new_attr.lower()
# change "MCSmatches" into "Mcs_matches" (it will then be
# converted to _mcs_matches by the code below)
new_attr = new_attr.replace("MCSmatches", "Mcs_matches")
# change "RDKit" to "Rdkit"
new_attr = new_attr.replace("RDKit", "Rdkit")
# change "MCS" into "Mcs" (it will then be converted to _mcs by
# the code below)
new_attr = new_attr.replace("MCS", "Mcs")
# change "MC" into "Mc" (it will be converted to _mc by the code below)
new_attr = new_attr.replace("MC", "Mc")
# change "aaBox" into "aabox"
new_attr = new_attr.replace("aaBox", "aabox")
# change "CONECT" to "Conect"
new_attr = new_attr.replace("CONECT", "Conect")
# change nSomething into num_somthing
m = re.match("^n([A-Z])[a-z]", new_attr)
if m:
new_attr = f"num_{m.groups()[0].lower()}{new_attr[2:]}"
# now change anyCapitalLetter into any_capital_letter
new_attr = "_".join(_upper_split(new_attr)).lower()
# remove any accidentally duplicated underscores
new_attr = new_attr.replace("__", "_")
if new_attr != attr:
try:
setattr(C, new_attr, getattr(C, attr))
if delete_old:
delattr(C, attr)
except Exception:
# this is a base-class function
pass
# need to do this in all of the bases too
# for B in C.mro():
# try:
# setattr(B, new_attr, getattr(B, attr))
#
# if delete_old:
# delattr(B, attr)
# except Exception:
# # this is not in the base class
# pass
def _pythonize_modules(modules, delete_old: bool = True):
"""Pythonize all classes in the passed module"""
for MOD in modules:
import inspect
try:
for key, cls in inspect.getmembers(MOD, inspect.isclass):
_pythonize(cls, delete_old=delete_old)
except Exception as e:
print(e)
print(f"Failed to pythonize {MOD}")
_is_using_old_api = None
_is_using_new_api = None
_is_in_loading_process = False
def _load_new_api_modules(delete_old: bool = True, is_base: bool = False):
"""
Internal function to load the new API modules, pythonizing
the function names as we go. If `delete_old` is True, then
the old function names will be deleted. Otherwise, they will
be kept. Keeping the names is only needed for the mixed API.
"""
global _is_using_new_api
_is_using_new_api = True
global _is_in_loading_process
if _is_in_loading_process:
return
_is_in_loading_process = True
# call Pythonize on all of the new modules
from .legacy import ( # noqa: F401
Base,
Mol,
Move,
IO,
System,
Squire,
MM,
FF,
Analysis,
CAS,
Cluster,
# doesn't need pythonizing but importing will make it visible
Convert,
Error,
ID,
Maths,
Qt,
Stream,
Units,
Vol,
)
_pythonize_modules(
[
Base._Base,
Analysis._Analysis,
CAS._CAS,
Cluster._Cluster,
Error._Error,
FF._FF,
ID._ID,
IO._IO,
Maths._Maths,
MM._MM,
Mol._Mol,
Move._Move,
Qt._Qt,
Squire._Squire,
Stream._Stream,
System._System,
Units._Units,
Vol._Vol,
],
delete_old=delete_old,
)
# Pythonize the QM classes.
_pythonize(Convert._SireOpenMM.PyQMCallback, delete_old=delete_old)
_pythonize(Convert._SireOpenMM.PyQMEngine, delete_old=delete_old)
_pythonize(Convert._SireOpenMM.PyQMForce, delete_old=delete_old)
_pythonize(Convert._SireOpenMM.TorchQMEngine, delete_old=delete_old)
_pythonize(Convert._SireOpenMM.TorchQMForce, delete_old=delete_old)
try:
import lazy_import
have_lazy_import = True
except ImportError:
have_lazy_import = False
if have_lazy_import:
# Now make sure that all new modules have been loaded
# (we need to import base first)
from . import base
if lazy_import.LazyModule in type(base).mro():
# this module is lazily loaded - use 'dir' to load it
dir(base)
if is_base:
# return, as we will only import base here
_is_in_loading_process = False
return
from . import (
move,
io,
system,
squire,
mm,
convert,
ff,
mol,
analysis,
cas,
cluster,
error,
id,
maths,
morph,
restraints,
qt,
stream,
units,
vol,
)
for M in [
move,
io,
system,
squire,
mm,
convert,
ff,
mol,
analysis,
cas,
cluster,
error,
id,
maths,
morph,
restraints,
qt,
stream,
units,
vol,
]:
if lazy_import.LazyModule in type(M).mro():
# this module is lazily loaded - use 'dir' to load it
dir(M)
_is_in_loading_process = False
[docs]
def use_mixed_api(support_old_module_names: bool = False):
"""Load Sire using both the new (python-style) and old APIs. This
is useful for migrating old scripts as a temporary porting option.
You can start writing functions using the new API, safe in the
knowledge that the old API functions will still work.
Do aim to finish your port though, else you will forever have
a duplicated API (e.g. have both X.nAtoms() and X.num_atoms() etc.)
"""
global _is_using_new_api, _is_using_old_api
if _is_using_old_api and _is_using_new_api:
# don't need to do this twice
return
if _is_using_old_api or _is_using_new_api:
msg = (
"Cannot import sire using the mixed API as either the old "
"or new APIs have already been activated."
)
print(msg)
raise ImportError(msg)
# First, bring in the old API
if support_old_module_names:
print("Loading Sire with support for old module names.")
print("Note that this can cause problems with classes importing twice.")
use_old_api()
else:
_is_using_old_api = True
# Now bring in the new API
_load_new_api_modules(delete_old=False)
[docs]
def use_new_api(is_base: bool = False):
"""
Load Sire using the new (python-style) API. This will be called
automatically when you load any of the new Python modules, so you
shouldn't need to call this yourself.
Parameters
----------
is_base: bool (defaults to False)
Whether or not this is being called by the sire.base module.
This triggers a special case where we only load sire.base,
and thus avoid circular imports
"""
global _is_using_new_api, _is_using_old_api
# load up the new console - ensure this is done once
from .utils import Console as _Console
_Console._get_console()
if _is_using_new_api:
# already done
return
if _is_using_old_api:
msg = (
"Cannot import sire using the new API as the old API has "
"already been activated. Both APIs cannot be active at "
"the same time."
)
print(msg)
raise ImportError(msg)
# Now bring in the new API
_load_new_api_modules(delete_old=True, is_base=is_base)
[docs]
def use_old_api():
"""Load Sire using the old (C++-style) API. This is for
compatibility reasons for old code only. This should
not be used with new code
"""
global _is_using_old_api, _is_using_new_api
if _is_using_new_api:
raise ImportError(
"Cannot import Sire using the old API as the new API has "
"already been activated. Both APIs cannot be active at "
"the same time."
)
if _is_using_old_api:
# already active
return
_is_using_old_api = True
from . import legacy
# set up the meta-importer with these modules - thanks to this post
# for all of the info
# https://dev.to/dangerontheranger/dependency-injection-with-import-hooks-in-python-3-5hap
import importlib.abc
import importlib.machinery
import sys
import types
class DependencyInjectorLoader(importlib.abc.Loader):
def __init__(self):
self._services = {}
self._dummy_module = types.ModuleType("Sire")
self._dummy_module.__path__ = []
def provide(self, service_name, module):
"""Register a service as provided via the given module
A service is any Python object in this context - an imported
module, a class, etc."""
self._services[service_name] = module
def provides(self, fullname):
if fullname in self._services:
return True
else:
return False
def create_module(self, spec):
"""Create the given module from the supplied module spec
Under the hood, this module returns a service or a dummy module,
depending on whether Python is still importing one of the names
listed in _COMMON_PREFIX.
"""
service_name = spec.name
if service_name not in self._services:
# return our dummy module since at this point we're loading
# *something* along the lines of "myapp.virtual" that's not
# a service
return self._dummy_module
module = self._services[service_name]
return module
def exec_module(self, module):
"""Execute the given module in its own namespace
This method is required to be present by importlib.abc.Loader,
but since we know our module object is already fully-formed,
this method merely no-ops.
"""
pass
class DependencyInjectorFinder(importlib.abc.MetaPathFinder):
def __init__(self, loader):
# we'll write the loader in a minute, hang tight
self._loader = loader
def find_spec(self, fullname, path, target=None):
"""Attempt to locate the requested module
fullname is the fully-qualified name of the module,
path is set to __path__ for sub-modules/packages, or None
otherwise target can be a module object, but is unused in this
example.
"""
if self._loader.provides(fullname):
return self._gen_spec(fullname)
def _gen_spec(self, fullname):
spec = importlib.machinery.ModuleSpec(fullname, self._loader)
return spec
class DependencyInjector:
"""
Convenience wrapper for DependencyInjectorLoader and
DependencyInjectorFinder.
"""
def __init__(self):
self._loader = DependencyInjectorLoader()
self._finder = DependencyInjectorFinder(self._loader)
def install(self):
sys.meta_path.append(self._finder)
def provide(self, service_name, module):
self._loader.provide(service_name, module)
injector = DependencyInjector()
# Use 'legacy' as a stand-in for Sire
injector.provide("Sire", legacy)
injector.install()